{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where technology = \"smartseq\" and tissue_curation = \"Eye\"", "rows": [[19087, "ERR13834862", "ERX13237628", "ERS21098715", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC1 S20 R1 001.fastq.gz", "SAMEA116100635", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 48 HC1", "webin reads 48 HC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC1_S20_R1_001.fastq.gz", "fastq", 3768442091.0, 38065677.0, "webin reads 48 HC1", "0:99.00", "A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200", 99, null, null, null, 1055463738, 792073627, 817607736, 1103223790, 73200, "ERX13237628", "ERS21098715", "ERA30883416", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19088, "ERR13834951", "ERX13237717", "ERS21098721", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC4 S31 R1 001.fastq.gz", "SAMEA116100646", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 58 AC4", "webin reads 58 AC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC4_S31_R1_001.fastq.gz", "fastq", 3607648651.0, 36331933.0, "webin reads 58 AC4", "0:99.30", "A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094", 99, null, null, null, 1038047870, 736262498, 759315202, 1073962987, 60094, "ERX13237776", "ERS21098726", "ERA30883721", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19090, "ERR13822794", "ERX13225546", "ERS21098708", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR2 S13 R1 001.fastq.gz", "48 PR2", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR2", "webin reads 48 PR2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR2_S13_R1_001.fastq.gz", "fastq", 3809299607.0, 38404185.0, "webin reads 48 PR2", "0:99.19", "A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777", 99, null, null, null, 1067728192, 802585802, 828435932, 1110435904, 113777, "ERX13225546", "ERS21098708", "ERA30879682", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19091, "ERR13834854", "ERX13237620", "ERS21098714", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC4 S19 R1 001.fastq.gz", "48 AC4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC4", "webin reads 48 AC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC4_S19_R1_001.fastq.gz", "fastq", 3410801894.0, 34443068.0, "webin reads 48 AC4", "0:99.03", "A:966160063;C:707754156;G:733039262;T:1003772756;N:75657", 99, null, null, null, 966160063, 707754156, 733039262, 1003772756, 75657, "ERX13237620", "ERS21098714", "ERA30883390", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19092, "ERR13828824", "ERX13231590", "ERS21098710", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR4 S15 R1 001.fastq.gz", "48 PR4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR4", "webin reads 48 PR4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR4_S15_R1_001.fastq.gz", "fastq", 4365943927.0, 44278278.0, "webin reads 48 PR4", "0:98.60", "A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503", 98, null, null, null, 1214448497, 927512154, 957491418, 1266385355, 106503, "ERX13231590", "ERS21098710", "ERA30883309", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19093, "ERR13834993", "ERX13237759", "ERS21098723", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC1 S28 R1 001.fastq.gz", "58 AC1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC1", "webin reads 58 AC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC1_S28_R1_001.fastq.gz", "fastq", 3710768269.0, 37364763.0, "webin reads 58 AC1", "0:99.31", "A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465", 99, null, null, null, 1060419097, 761984557, 786533722, 1101603428, 227465, "ERX13237759", "ERS21098723", "ERA30883659", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19094, "ERR13834875", "ERX13237641", "ERS21098717", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC3 S22 R1 001.fastq.gz", "48 HC3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 HC3", "webin reads 48 HC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC3_S22_R1_001.fastq.gz", "fastq", 3083078586.0, 31073491.0, "webin reads 48 HC3", "0:99.22", "A:856250957;C:655140994;G:677078911;T:894558582;N:49142", 99, null, null, null, 856250957, 655140994, 677078911, 894558582, 49142, "ERX13237641", "ERS21098717", "ERA30883447", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19095, "ERR13834899", "ERX13237665", "ERS21098720", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR2 S25 R1 001.fastq.gz", "58 PR2", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR2", "webin reads 58 PR2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR2_S25_R1_001.fastq.gz", "fastq", 3849571818.0, 38706841.0, "webin reads 58 PR2", "0:99.45", "A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547", 99, null, null, null, 1089593011, 803322469, 827777017, 1128836774, 42547, "ERX13237665", "ERS21098720", "ERA30883518", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19096, "ERR13834889", "ERX13237655", "ERS21098719", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR1 S24 R1 001.fastq.gz", "58 PR1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR1", "webin reads 58 PR1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR1_S24_R1_001.fastq.gz", "fastq", 3945671240.0, 39514922.0, "webin reads 58 PR1", "0:99.85", "A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802", 99, null, null, null, 1135075173, 807489123, 827964380, 1175109762, 32802, "ERX13237655", "ERS21098719", "ERA30883497", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19097, "ERR13835019", "ERX13237785", "ERS21098728", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC2 S33 R1 001.fastq.gz", "SAMEA116100648", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 58 HC2", "webin reads 58 HC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC2_S33_R1_001.fastq.gz", "fastq", 3711237069.0, 37217240.0, "webin reads 58 HC2", "0:99.72", "A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762", 99, null, null, null, 1070592288, 757099665, 780689044, 1102575310, 280762, "ERX13237785", "ERS21098728", "ERA30883748", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19098, "ERR13822110", "ERX13224862", "ERS21098697", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38PR2 S2 R1 001.fastq.gz", "38 PR2", null, "organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 PR2", "webin reads 38 PR2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 PR2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38PR2_S2_R1_001.fastq.gz", "fastq", 3463281109.0, 34821985.0, "webin reads 38 PR2", "0:99.46", "A:969862466;C:733798241;G:755135957;T:1004440555;N:43890", 99, null, null, null, 969862466, 733798241, 755135957, 1004440555, 43890, "ERX13224862", "ERS21098697", "ERA30879238", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19099, "ERR13822784", "ERX13225536", "ERS21098706", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38HC3 S11 R1 001.fastq.gz", "38 HC3", null, "organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 HC3", "webin reads 38 HC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 HC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38HC3_S11_R1_001.fastq.gz", "fastq", 4360921873.0, 44107486.0, "webin reads 38 HC3", "0:98.87", "A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882", 98, null, null, null, 1222778761, 918257887, 948838973, 1270939370, 106882, "ERX13225536", "ERS21098706", "ERA30879613", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19100, "ERR13828836", "ERX13231602", "ERS21098712", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC2 S17 R1 001.fastq.gz", "48 AC2", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC2", "webin reads 48 AC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC2_S17_R1_001.fastq.gz", "fastq", 3205206588.0, 32424632.0, "webin reads 48 AC2", "0:98.85", "A:902438127;C:672433401;G:694813369;T:935445436;N:76255", 98, null, null, null, 902438127, 672433401, 694813369, 935445436, 76255, "ERX13231602", "ERS21098712", "ERA30883343", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19101, "ERR13835004", "ERX13237770", "ERS21098725", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC3 S30 R1 001.fastq.gz", "58 AC3", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC3", "webin reads 58 AC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC3_S30_R1_001.fastq.gz", "fastq", 3782993133.0, 38295959.0, "webin reads 58 AC3", "0:98.78", "A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531", 98, null, null, null, 1080745150, 779903026, 803258485, 1118994941, 91531, "ERX13237770", "ERS21098725", "ERA30883697", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19102, "ERR13834868", "ERX13237634", "ERS21098716", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC2 S21 R1 001.fastq.gz", "SAMEA116100636", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 48 HC2", "webin reads 48 HC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC2_S21_R1_001.fastq.gz", "fastq", 3424347865.0, 34510204.0, "webin reads 48 HC2", "0:99.23", "A:959488173;C:721171249;G:745705870;T:997922014;N:60559", 99, null, null, null, 959488173, 721171249, 745705870, 997922014, 60559, "ERX13237634", "ERS21098716", "ERA30883434", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19103, "ERR13822197", "ERX13224949", "ERS21098704", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38HC1 S9 R1 001.fastq.gz", "SAMEA116100624", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 38 HC1", "webin reads 38 HC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 HC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38HC1_S9_R1_001.fastq.gz", "fastq", 3784641498.0, 38331162.0, "webin reads 38 HC1", "0:98.74", "A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167", 98, null, null, null, 1064199311, 791310791, 818910597, 1110118632, 102167, "ERX13224949", "ERS21098704", "ERA30879548", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19104, "ERR13834880", "ERX13237646", "ERS21098718", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC4 S23 R1 001.fastq.gz", "48 HC4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 HC4", "webin reads 48 HC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC4_S23_R1_001.fastq.gz", "fastq", 3660674315.0, 36821474.0, "webin reads 48 HC4", "0:99.42", "A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267", 99, null, null, null, 1035049987, 763030378, 788062167, 1074303516, 228267, "ERX13237646", "ERS21098718", "ERA30883470", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19105, "ERR13822867", "ERX13225633", "ERS21098709", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR3 S14 R1 001.fastq.gz", "48 PR3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR3", "webin reads 48 PR3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR3_S14_R1_001.fastq.gz", "fastq", 4232170464.0, 42534853.0, "webin reads 48 PR3", "0:99.50", "A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079", 99, null, null, null, 1195251409, 889346003, 917240118, 1230272855, 60079, "ERX13225633", "ERS21098709", "ERA30879704", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19106, "ERR13822131", "ERX13224883", "ERS21098700", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38AC1 S5 R1 001.fastq.gz", "SAMEA116100620", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 38 AC1", "webin reads 38 AC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 AC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38AC1_S5_R1_001.fastq.gz", "fastq", 3836921113.0, 38702139.0, "webin reads 38 AC1", "0:99.14", "A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693", 99, null, null, null, 1066720805, 818958589, 843762182, 1107403844, 75693, "ERX13224883", "ERS21098700", "ERA30879356", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19107, "ERR13822143", "ERX13224895", "ERS21098702", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38AC3 S7 R1 001.fastq.gz", "38 AC3", null, "organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 AC3", "webin reads 38 AC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 AC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38AC3_S7_R1_001.fastq.gz", "fastq", 3452707377.0, 34902410.0, "webin reads 38 AC3", "0:98.92", "A:970868997;C:726795179;G:750560378;T:1004408693;N:74130", 98, null, null, null, 970868997, 726795179, 750560378, 1004408693, 74130, "ERX13224895", "ERS21098702", "ERA30879451", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19108, "ERR13828843", "ERX13234350", "ERS21098713", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC3 S18 R1 001.fastq.gz", "48 AC3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC3", "webin reads 48 AC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC3_S18_R1_001.fastq.gz", "fastq", 3733628911.0, 37779462.0, "webin reads 48 AC3", "0:98.83", "A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473", 98, null, null, null, 1047204450, 786943605, 812327274, 1086893109, 260473, "ERX13234350", "ERS21098713", "ERA30883366", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19109, "ERR13822153", "ERX13224905", "ERS21098703", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38AC4 S8 R1 001.fastq.gz", "38 AC4", null, "organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 AC4", "webin reads 38 AC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 AC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38AC4_S8_R1_001.fastq.gz", "fastq", 4130629624.0, 41794865.0, "webin reads 38 AC4", "0:98.83", "A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277", 98, null, null, null, 1156746387, 877063962, 905379690, 1191264308, 175277, "ERX13224905", "ERS21098703", "ERA30879532", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19110, "ERR13822201", "ERX13224953", "ERS21098705", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38HC2 S10 R1 001.fastq.gz", "38 HC2", null, "organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 HC2", "webin reads 38 HC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 HC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38HC2_S10_R1_001.fastq.gz", "fastq", 4221340137.0, 42584743.0, "webin reads 38 HC2", "0:99.13", "A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761", 99, null, null, null, 1195817135, 879958039, 908085464, 1237394738, 84761, "ERX13224953", "ERS21098705", "ERA30879582", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19111, "ERR13822114", "ERX13224866", "ERS21098698", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38PR3 S3 R1 001.fastq.gz", "SAMEA116100618", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 38 PR3", "webin reads 38 PR3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 PR3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38PR3_S3_R1_001.fastq.gz", "fastq", 3894010106.0, 39196855.0, "webin reads 38 PR3", "0:99.34", "A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488", 99, null, null, null, 1093221995, 818047738, 843661747, 1138957138, 121488, "ERX13224866", "ERS21098698", "ERA30879273", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19112, "ERR13822135", "ERX13224887", "ERS21098701", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38AC2 S6 R1 001.fastq.gz", "38 AC2", null, "organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 AC2", "webin reads 38 AC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 AC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38AC2_S6_R1_001.fastq.gz", "fastq", 3913343007.0, 39682834.0, "webin reads 38 AC2", "0:98.62", "A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960", 98, null, null, null, 1089960083, 827936673, 855955684, 1139372607, 117960, "ERX13224887", "ERS21098701", "ERA30879382", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19113, "ERR13835032", "ERX13237798", "ERS21098730", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC4 S35 R1 001.fastq.gz", "58 HC4", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC4", "webin reads 58 HC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC4_S35_R1_001.fastq.gz", "fastq", 4418556015.0, 44331835.0, "webin reads 58 HC4", "0:99.67", "A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918", 99, null, null, null, 1255080581, 916490847, 946212615, 1300735054, 36918, "ERX13237798", "ERS21098730", "ERA30883773", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19114, "ERR13828829", "ERX13231595", "ERS21098711", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC1 S16 R1 001.fastq.gz", "48 AC1", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC1", "webin reads 48 AC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC1_S16_R1_001.fastq.gz", "fastq", 3933669121.0, 39695406.0, "webin reads 48 AC1", "0:99.10", "A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068", 99, null, null, null, 1105258159, 824538054, 854253688, 1149538152, 81068, "ERX13231595", "ERS21098711", "ERA30883326", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19115, "ERR13822099", "ERX13224851", "ERS21098696", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38PR1 S1 R1 001.fastq.gz", "38 PR1", null, "organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 PR1", "webin reads 38 PR1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 PR1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38PR1_S1_R1_001.fastq.gz", "fastq", 4256158288.0, 42658127.0, "webin reads 38 PR1", "0:99.77", "A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845", 99, null, null, null, 1193880575, 899261652, 926114030, 1236860186, 41845, "ERX13224851", "ERS21098696", "ERA30879152", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19116, "ERR13822119", "ERX13224871", "ERS21098699", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38PR4 S4 R1 001.fastq.gz", "38 PR4", null, "organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 PR4", "webin reads 38 PR4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 PR4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38PR4_S4_R1_001.fastq.gz", "fastq", 3726308046.0, 37591038.0, "webin reads 38 PR4", "0:99.13", "A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180", 99, null, null, null, 1043231302, 789255840, 812957881, 1080801843, 61180, "ERX13224871", "ERS21098699", "ERA30879302", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19117, "ERR13835025", "ERX13237791", "ERS21098729", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC3 S34 R1 001.fastq.gz", "58 HC3", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC3", "webin reads 58 HC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC3_S34_R1_001.fastq.gz", "fastq", 3523899212.0, 35292613.0, "webin reads 58 HC3", "0:99.85", "A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640", 99, null, null, null, 1012516999, 723225071, 745152410, 1042976092, 28640, "ERX13237791", "ERS21098729", "ERA30883757", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19118, "ERR13835014", "ERX13237780", "ERS21098727", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC1 S32 R1 001.fastq.gz", "58 HC1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC1", "webin reads 58 HC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC1_S32_R1_001.fastq.gz", "fastq", 3436493821.0, 34597887.0, "webin reads 58 HC1", "0:99.33", "A:980894291;C:707196785;G:729948858;T:1018400124;N:53763", 99, null, null, null, 980894291, 707196785, 729948858, 1018400124, 53763, "ERX13237780", "ERS21098727", "ERA30883731", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19119, "ERR13834987", "ERX13237753", "ERS21098722", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR4 S27 R1 001.fastq.gz", "58 PR4", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR4", "webin reads 58 PR4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR4_S27_R1_001.fastq.gz", "fastq", 3069040814.0, 30923422.0, "webin reads 58 PR4", "0:99.25", "A:875776938;C:633951750;G:653308475;T:905949639;N:54012", 99, null, null, null, 875776938, 633951750, 653308475, 905949639, 54012, "ERX13237753", "ERS21098722", "ERA30883641", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19120, "ERR13822788", "ERX13225540", "ERS21098707", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "38HC4 S12 R1 001.fastq.gz", "38 HC4", null, "organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 38 HC4", "webin reads 38 HC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 38 HC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "38HC4_S12_R1_001.fastq.gz", "fastq", 3353994440.0, 33744828.0, "webin reads 38 HC4", "0:99.39", "A:939537209;C:709367668;G:731849729;T:973193819;N:46015", 99, null, null, null, 939537209, 709367668, 731849729, 973193819, 46015, "ERX13225540", "ERS21098707", "ERA30879650", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Pharyngula", "Embryo", "Eye", "Sensory System"], [19121, "ERR13834997", "ERX13237763", "ERS21098724", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC2 S29 R1 001.fastq.gz", "58 AC2", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC2", "webin reads 58 AC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC2_S29_R1_001.fastq.gz", "fastq", 3872162091.0, 38898173.0, "webin reads 58 AC2", "0:99.55", "A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918", 99, null, null, null, 1111663794, 793747086, 817730996, 1148980297, 39918, "ERX13237763", "ERS21098724", "ERA30883678", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [30572, "SRR27848813", "SRX23511754", "SRS20362222", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 7", "GSM8061015", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 7", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061015", "GSM8061015: Wildtype 7; Danio rerio; RNA Seq", "GSM8061015 r1", "GSM8061015", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT7_1.fq.gz WT7_2.fq.gz", "fastq fastq", 16387213200.0, 54624044.0, "GSM8061015 r1", "0:150 1:150", "A:4787207224;C:3312386758;G:3384738324;T:4902574775;N:306119", 150, 150, null, null, 4787207224, 3312386758, 3384738324, 4902574775, 306119, "SRX23511754", "SRS20362222", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.92431, 0.91825, 0.16903, 0.16976, 0.74067, 0.75189, 0.50167, 0.50261, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30573, "SRR27848814", "SRX23511753", "SRS20362221", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 6", "GSM8061014", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 6", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061014", "GSM8061014: Wildtype 6; Danio rerio; RNA Seq", "GSM8061014 r1", "GSM8061014", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT6_1.fq.gz WT6_2.fq.gz", "fastq fastq", 19114278900.0, 63714263.0, "GSM8061014 r1", "0:150 1:150", "A:5885874877;C:3513555230;G:3610119151;T:6104379853;N:349789", 150, 150, null, null, 5885874877, 3513555230, 3610119151, 6104379853, 349789, "SRX23511753", "SRS20362221", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88104, 0.87237, 0.33066, 0.33508, 0.7357, 0.7499, 0.52706, 0.51369, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30574, "SRR27848815", "SRX23511752", "SRS20362220", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 5", "GSM8061013", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 5", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061013", "GSM8061013: Wildtype 5; Danio rerio; RNA Seq", "GSM8061013 r1", "GSM8061013", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT5_2.fq.gz WT5_1.fq.gz", "fastq fastq", 16120305900.0, 53734353.0, "GSM8061013 r1", "0:150 1:150", "A:4774586081;C:3152393582;G:3245217813;T:4947808687;N:299737", 150, 150, null, null, 4774586081, 3152393582, 3245217813, 4947808687, 299737, "SRX23511752", "SRS20362220", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.90351, 0.89372, 0.19598, 0.19188, 0.74468, 0.76037, 0.49643, 0.5012, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30575, "SRR27848816", "SRX23511751", "SRS20362219", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 4", "GSM8061012", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 4", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061012", "GSM8061012: Wildtype 4; Danio rerio; RNA Seq", "GSM8061012 r1", "GSM8061012", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT4_1.fq.gz WT4_2.fq.gz", "fastq fastq", 15545813700.0, 51819379.0, "GSM8061012 r1", "0:150 1:150", "A:4735339999;C:2883223993;G:2979819364;T:4947148649;N:281695", 150, 150, null, null, 4735339999, 2883223993, 2979819364, 4947148649, 281695, "SRX23511751", "SRS20362219", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88431, 0.87409, 0.2472, 0.24596, 0.74675, 0.76534, 0.50472, 0.51348, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30576, "SRR27848817", "SRX23511750", "SRS20362218", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 3", "GSM8061011", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 3", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061011", "GSM8061011: Wildtype 3; Danio rerio; RNA Seq", "GSM8061011 r1", "GSM8061011", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT3_1.fq.gz WT3_2.fq.gz", "fastq fastq", 17883593700.0, 59611979.0, "GSM8061011 r1", "0:150 1:150", "A:5305029339;C:3503937995;G:3594774195;T:5479523425;N:328746", 150, 150, null, null, 5305029339, 3503937995, 3594774195, 5479523425, 328746, "SRX23511750", "SRS20362218", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.90376, 0.89786, 0.22127, 0.22019, 0.72941, 0.74257, 0.49283, 0.4977, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30577, "SRR27848818", "SRX23511749", "SRS20362217", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 2", "GSM8061010", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 2", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061010", "GSM8061010: Wildtype 2; Danio rerio; RNA Seq", "GSM8061010 r1", "GSM8061010", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT2_1.fq.gz WT2_2.fq.gz", "fastq fastq", 15921002400.0, 53070008.0, "GSM8061010 r1", "0:150 1:150", "A:4801739158;C:2898179014;G:3037454009;T:5183338180;N:292039", 150, 150, null, null, 4801739158, 2898179014, 3037454009, 5183338180, 292039, "SRX23511749", "SRS20362217", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88935, 0.87616, 0.22376, 0.2085, 0.75367, 0.78123, 0.53443, 0.51122, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30578, "SRR27848819", "SRX23511748", "SRS20362216", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Wildtype 1", "GSM8061009", null, "source name:Retina|tissue:Retina|genotype:Wildtype|geo loc name:missing|collection date:missing", "Wildtype 1", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Wildtype", "GSM8061009", "GSM8061009: Wildtype 1; Danio rerio; RNA Seq", "GSM8061009 r1", "GSM8061009", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "WT1_1.fq.gz WT1_2.fq.gz", "fastq fastq", 15664926900.0, 52216423.0, "GSM8061009 r1", "0:150 1:150", "A:4654413024;C:3082161368;G:3150203371;T:4777859952;N:289185", 150, 150, null, null, 4654413024, 3082161368, 3150203371, 4777859952, 289185, "SRX23511748", "SRS20362216", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.9012, 0.89646, 0.22096, 0.21863, 0.73507, 0.7475, 0.4816, 0.4726, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30579, "SRR27848820", "SRX23511747", "SRS20362215", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 7", "GSM8061008", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 7", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061008", "GSM8061008: Choroideremia 7; Danio rerio; RNA Seq", "GSM8061008 r1", "GSM8061008", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM7_2.fq.gz CHM7_1.fq.gz", "fastq fastq", 16991281200.0, 56637604.0, "GSM8061008 r1", "0:150 1:150", "A:4896856485;C:3497447652;G:3598783228;T:4998138764;N:55071", 150, 150, null, null, 4896856485, 3497447652, 3598783228, 4998138764, 55071, "SRX23511747", "SRS20362215", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.926, 0.92518, 0.16779, 0.16551, 0.72393, 0.73513, 0.51723, 0.51214, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30580, "SRR27848821", "SRX23511746", "SRS20362214", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 6", "GSM8061007", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 6", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061007", "GSM8061007: Choroideremia 6; Danio rerio; RNA Seq", "GSM8061007 r1", "GSM8061007", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM6_1.fq.gz CHM6_2.fq.gz", "fastq fastq", 18881901900.0, 62939673.0, "GSM8061007 r1", "0:150 1:150", "A:5796692721;C:3348140904;G:3547934333;T:6189072751;N:61191", 150, 150, null, null, 5796692721, 3348140904, 3547934333, 6189072751, 61191, "SRX23511746", "SRS20362214", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.86869, 0.86484, 0.26053, 0.2569, 0.75057, 0.77705, 0.66121, 0.65975, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30581, "SRR27848822", "SRX23511745", "SRS20362213", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 5", "GSM8061006", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 5", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061006", "GSM8061006: Choroideremia 5; Danio rerio; RNA Seq", "GSM8061006 r1", "GSM8061006", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM5_2.fq.gz CHM5_1.fq.gz", "fastq fastq", 17802156900.0, 59340523.0, "GSM8061006 r1", "0:150 1:150", "A:5198674613;C:3599354426;G:3698229931;T:5305840019;N:57911", 150, 150, null, null, 5198674613, 3599354426, 3698229931, 5305840019, 57911, "SRX23511745", "SRS20362213", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.9109, 0.91251, 0.18901, 0.18793, 0.72354, 0.73456, 0.51839, 0.52348, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30582, "SRR27848823", "SRX23511744", "SRS20362212", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 4", "GSM8061005", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 4", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061005", "GSM8061005: Choroideremia 4; Danio rerio; RNA Seq", "GSM8061005 r1", "GSM8061005", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM4_2.fq.gz CHM4_1.fq.gz", "fastq fastq", 15944831400.0, 53149438.0, "GSM8061005 r1", "0:150 1:150", "A:4833633886;C:2870981386;G:3055307522;T:5184819306;N:89300", 150, 150, null, null, 4833633886, 2870981386, 3055307522, 5184819306, 89300, "SRX23511744", "SRS20362212", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88929, 0.88364, 0.25277, 0.24996, 0.75317, 0.77826, 0.64914, 0.65907, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30583, "SRR27848824", "SRX23511743", "SRS20362211", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 3", "GSM8061004", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 3", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061004", "GSM8061004: Choroideremia 3; Danio rerio; RNA Seq", "GSM8061004 r1", "GSM8061004", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM3_1.fq.gz CHM3_2.fq.gz", "fastq fastq", 16028608800.0, 53428696.0, "GSM8061004 r1", "0:150 1:150", "A:4842495383;C:2966448486;G:3084331699;T:5135033798;N:299434", 150, 150, null, null, 4842495383, 2966448486, 3084331699, 5135033798, 299434, "SRX23511743", "SRS20362211", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.89747, 0.88445, 0.23706, 0.23597, 0.72904, 0.75187, 0.5514, 0.45471, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30584, "SRR27848825", "SRX23511742", "SRS20362210", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 2", "GSM8061003", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 2", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061003", "GSM8061003: Choroideremia 2; Danio rerio; RNA Seq", "GSM8061003 r1", "GSM8061003", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM2_1.fq.gz CHM2_2.fq.gz", "fastq fastq", 14968884300.0, 49896281.0, "GSM8061003 r1", "0:150 1:150", "A:4575866591;C:2606132581;G:2819446784;T:4967389772;N:48572", 150, 150, null, null, 4575866591, 2606132581, 2819446784, 4967389772, 48572, "SRX23511742", "SRS20362210", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.88022, 0.87326, 0.29312, 0.29812, 0.7335, 0.76228, 0.5854, 0.57614, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [30585, "SRR27848826", "SRX23511741", "SRS20362209", "SRP487850", "PRJNA1072679", "Oxidative stress altered glucose metabolism and inflammation contribute to the retinal phenotype in the choroideremia zebrafish", "GSE254948", "Transcriptome Analysis", "Reactive oxygen species ROS within the retina play a key role in maintaining function and cell survival. However excessive ROS can lead to oxidative stress inducing dysregulation of metabolic and inflammatory pathways. The chmru848 zebrafish models choroideremia CHM an X linked chorioretinal dystrophy which predominantly affects the photoreceptors retinal pigment epithelium RPE and choroid. In this study we examined the transcriptomic signature of the chmru848 zebrafish retina to reveal upregulation of cytokine pathways and glia migration upregulation of oxidative ER stress and apoptosis markers and dysregulation of glucose metabolism with downregulation of glycolysis and upregulation of the oxidative phase of the pentose phosphate pathway. Glucose uptake was overall impaired in the chmru848 retina using the 2 NBDG glucose uptake assay but post overexpression of human PFKM it partially rescued the retinal phenotype and glucose uptake but without xxx the expression of glycolysis markers. Therapies targeting glucose metabolism in CHM may represent a potential remedial approach. Overall design: Choroideremia CHM is a x linked inherited retinal dystrophy caused by mutations in the CHM gene. It is a progressive condition leading to complete blindness. We are working on a chm zebrafish model which shows a widespread severe degenerative phenotype with embryos only surviving up to 5 days. We compared the transcriptome in wildtype vs chm zebrafish retinas and determine which pathways are disrupted in chm fish.", null, null, null, "Choroideremia 1", "GSM8061002", null, "source name:Retina|tissue:Retina|genotype:Choroideremia|geo loc name:missing|collection date:missing", "Choroideremia 1", "Raw reads were quality and adapter trimmed using trimgalore version 0.6.7 14 before alignment. Reads were mapped and subsequent gene level counted using RSEM 1.3.3 15 and STAR 2.7.10a 16 against the zebrafish genome GRCz11 both from Ensembl. Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package version 1.38.3within the R programming environment version 4.2.2. Assembly: GRCz11 Supplementary files format and content: VST normalised expression values. Rows = genes; Columns = samples.", "Retina", null, "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "tissue:Retina|genotype:Choroideremia", "GSM8061002", "GSM8061002: Choroideremia 1; Danio rerio; RNA Seq", "GSM8061002 r1", "GSM8061002", "1", "Bulk RNA was extracted with RNAeasy Micro Plus kit Qiagen from chmru848 and wt control retinas n=7 per group and high RNA quality was confirmed by Agilent 2100 Bioanalyzer G2939A cDNA libraries were subsequently constructed from total RNA RIN \u2265 8 using the Clontech SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP487850", null, "loader:fastq load.py", "CHM1_2.fq.gz CHM1_1.fq.gz", "fastq fastq", 15862639500.0, 52875465.0, "GSM8061002 r1", "0:150 1:150", "A:4812544148;C:2881706406;G:3014671171;T:5153419977;N:297798", 150, 150, null, null, 4812544148, 2881706406, 3014671171, 5153419977, 297798, "SRX23511741", "SRS20362209", "SRA1796957", "The Francis Crick Institute", "The Francis Crick Institute", 2, 0.89157, 0.87804, 0.24616, 0.24284, 0.73884, 0.76232, 0.58251, 0.58918, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2024-02-02", "Undetermined", "Embryo", "Eye", "Sensory System"], [33304, "SRR29927538", "SRX25421512", "SRS22081668", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "INL 3d rep2", "MCWR 2019 000138", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer", "INL 3d rep2", "INL 3d rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000138_S10_L001_R1_001.fastq.gz MCWR_2019_000138_S10_L001_R2_001.fastq.gz MCWR_2019_000138_S10_L002_R1_001.fastq.gz MCWR_2019_000138_S10_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 12792286105.0, 42489107.0, "MCWR 2019 000138 S10 L001 R1 001.fastq.gz", "0:150.53 1:150.54", "A:3362192057;C:3017281691;G:3072735924;T:3339916027;N:160406", 150, 150, null, null, 3362192057, 3017281691, 3072735924, 3339916027, 160406, "SRX25421512", "SRS22081668", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95023, 0.94904, 0.10306, 0.10406, 0.71167, 0.71305, 0.46929, 0.47143, 149, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33305, "SRR29927539", "SRX25421511", "SRS22081667", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "INL 3d rep1", "MCWR 2019 000137", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL 3d rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury inner nuclear layer", "INL 3d rep1", "INL 3d rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000137_S9_L001_R1_001.fastq.gz MCWR_2019_000137_S9_L001_R2_001.fastq.gz MCWR_2019_000137_S9_L002_R1_001.fastq.gz MCWR_2019_000137_S9_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11290383949.0, 37500632.0, "MCWR 2019 000137 S9 L001 R1 001.fastq.gz", "0:150.53 1:150.54", "A:2978304239;C:2650227687;G:2709306614;T:2952404306;N:141103", 150, 150, null, null, 2978304239, 2650227687, 2709306614, 2952404306, 141103, "SRX25421511", "SRS22081667", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95037, 0.94915, 0.09395, 0.0939, 0.71019, 0.71143, 0.47425, 0.46854, 151, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33306, "SRR29927540", "SRX25421510", "SRS22081666", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "INL Control rep3", "MCWR 2019 000136", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive inner nuclear layer", "INL Control rep3", "INL Control rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000136_S8_L001_R1_001.fastq.gz MCWR_2019_000136_S8_L001_R2_001.fastq.gz MCWR_2019_000136_S8_L002_R1_001.fastq.gz MCWR_2019_000136_S8_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 10926876847.0, 36289612.0, "MCWR 2019 000136 S8 L001 R1 001.fastq.gz", "0:150.54 1:150.56", "A:2876719537;C:2534137531;G:2628404662;T:2887478941;N:136176", 150, 150, null, null, 2876719537, 2534137531, 2628404662, 2887478941, 136176, "SRX25421510", "SRS22081666", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.9413, 0.94085, 0.12465, 0.12554, 0.71565, 0.71536, 0.47866, 0.47866, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33307, "SRR29927541", "SRX25421509", "SRS22081665", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "INL Control rep2", "MCWR 2019 000135", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive inner nuclear layer", "INL Control rep2", "INL Control rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000135_S7_L001_R1_001.fastq.gz MCWR_2019_000135_S7_L001_R2_001.fastq.gz MCWR_2019_000135_S7_L002_R1_001.fastq.gz MCWR_2019_000135_S7_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11015573968.0, 36586451.0, "MCWR 2019 000135 S7 L001 R1 001.fastq.gz", "0:150.54 1:150.54", "A:2922133009;C:2558945272;G:2631247657;T:2903110333;N:137697", 150, 150, null, null, 2922133009, 2558945272, 2631247657, 2903110333, 137697, "SRX25421509", "SRS22081665", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.94458, 0.94452, 0.1088, 0.10943, 0.71167, 0.71161, 0.48464, 0.48393, 149, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33308, "SRR29927542", "SRX25421508", "SRS22081664", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "INL Control rep1", "MCWR 2019 000134", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:INL Control rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive inner nuclear layer", "INL Control rep1", "INL Control rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000134_S6_L001_R1_001.fastq.gz MCWR_2019_000134_S6_L001_R2_001.fastq.gz MCWR_2019_000134_S6_L002_R1_001.fastq.gz MCWR_2019_000134_S6_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 12065204348.0, 40074475.0, "MCWR 2019 000134 S6 L001 R1 001.fastq.gz", "0:150.53 1:150.54", "A:3229181479;C:2787700756;G:2849413410;T:3198752940;N:155763", 150, 150, null, null, 3229181479, 2787700756, 2849413410, 3198752940, 155763, "SRX25421508", "SRS22081664", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.94249, 0.94233, 0.10755, 0.10774, 0.71427, 0.71449, 0.48361, 0.48286, 151, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33309, "SRR29927543", "SRX25421507", "SRS22081663", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "GCL 3d rep3", "MCWR 2019 000133", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer", "GCL 3d rep3", "GCL 3d rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000133_S5_L001_R1_001.fastq.gz MCWR_2019_000133_S5_L001_R2_001.fastq.gz MCWR_2019_000133_S5_L002_R1_001.fastq.gz MCWR_2019_000133_S5_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11567455830.0, 38423805.0, "MCWR 2019 000133 S5 L001 R1 001.fastq.gz", "0:150.52 1:150.52", "A:3334076845;C:2423637444;G:2488288638;T:3321309876;N:143027", 150, 150, null, null, 3334076845, 2423637444, 2488288638, 3321309876, 143027, "SRX25421507", "SRS22081663", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.90351, 0.90273, 0.20071, 0.20036, 0.7443, 0.74588, 0.57805, 0.58483, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33310, "SRR29927544", "SRX25421506", "SRS22081662", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "GCL 3d rep2", "MCWR 2019 000132", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer", "GCL 3d rep2", "GCL 3d rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000132_S4_L001_R1_001.fastq.gz MCWR_2019_000132_S4_L001_R2_001.fastq.gz MCWR_2019_000132_S4_L002_R1_001.fastq.gz MCWR_2019_000132_S4_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9928742591.0, 32979607.0, "MCWR 2019 000132 S4 L001 R1 001.fastq.gz", "0:150.53 1:150.53", "A:2670122365;C:2289339998;G:2333968379;T:2635186637;N:125212", 150, 150, null, null, 2670122365, 2289339998, 2333968379, 2635186637, 125212, "SRX25421506", "SRS22081662", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.94453, 0.9429, 0.1039, 0.10476, 0.72032, 0.72184, 0.51703, 0.51652, 148, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33313, "SRR29927547", "SRX25421503", "SRS22081659", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "GCL 3d rep1", "MCWR 2019 000131", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL 3d rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury ganglion cell layer", "GCL 3d rep1", "GCL 3d rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000131_S3_L001_R1_001.fastq.gz MCWR_2019_000131_S3_L001_R2_001.fastq.gz MCWR_2019_000131_S3_L002_R1_001.fastq.gz MCWR_2019_000131_S3_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11040747879.0, 36674133.0, "MCWR 2019 000131 S3 L001 R1 001.fastq.gz", "0:150.52 1:150.53", "A:3033865749;C:2483236067;G:2540109846;T:2983395404;N:140813", 150, 150, null, null, 3033865749, 2483236067, 2540109846, 2983395404, 140813, "SRX25421503", "SRS22081659", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.9328, 0.93075, 0.12255, 0.12345, 0.72675, 0.72949, 0.52776, 0.53024, 150, 149, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33318, "SRR29927552", "SRX25421498", "SRS22081654", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL 3d rep3", "MCWR 2019 000145", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer", "ONL 3d rep3", "ONL 3d rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000145_S16_L001_R1_001.fastq.gz MCWR_2019_000145_S16_L001_R2_001.fastq.gz MCWR_2019_000145_S16_L002_R1_001.fastq.gz MCWR_2019_000145_S16_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11434401733.0, 37973868.0, "MCWR 2019 000145 S16 L001 R1 001.fastq.gz", "0:150.56 1:150.55", "A:2952068036;C:2779158705;G:2786796140;T:2916234156;N:144696", 150, 150, null, null, 2952068036, 2779158705, 2786796140, 2916234156, 144696, "SRX25421498", "SRS22081654", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95416, 0.95385, 0.07766, 0.07806, 0.79024, 0.78989, 0.40138, 0.42872, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33319, "SRR29927553", "SRX25421497", "SRS22081653", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL 3d rep2", "MCWR 2019 000144", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer", "ONL 3d rep2", "ONL 3d rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000144_S15_L002_R2_001.fastq.gz MCWR_2019_000144_S15_L002_R1_001.fastq.gz MCWR_2019_000144_S15_L001_R2_001.fastq.gz MCWR_2019_000144_S15_L001_R1_001.fastq.gz", "fastq fastq fastq fastq", 10784131193.0, 35816254.0, "MCWR 2019 000144 S15 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:2770521598;C:2622163802;G:2642603869;T:2748709177;N:132747", 150, 150, null, null, 2770521598, 2622163802, 2642603869, 2748709177, 132747, "SRX25421497", "SRS22081653", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95823, 0.9574, 0.06867, 0.06894, 0.77055, 0.77234, 0.43067, 0.43052, 149, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33320, "SRR29927554", "SRX25421496", "SRS22081652", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL 3d rep1", "MCWR 2019 000143", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL 3d rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: 3 day post optic nerve injury outer nuclear layer", "ONL 3d rep1", "ONL 3d rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000143_S14_L001_R1_001.fastq.gz MCWR_2019_000143_S14_L001_R2_001.fastq.gz MCWR_2019_000143_S14_L002_R1_001.fastq.gz MCWR_2019_000143_S14_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 10414222985.0, 34587231.0, "MCWR 2019 000143 S14 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:2640548677;C:2562227240;G:2582839755;T:2628478265;N:129048", 150, 150, null, null, 2640548677, 2562227240, 2582839755, 2628478265, 129048, "SRX25421496", "SRS22081652", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95893, 0.95898, 0.06693, 0.06725, 0.78216, 0.7833, 0.41018, 0.40065, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33321, "SRR29927555", "SRX25421495", "SRS22081651", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL Control rep3", "MCWR 2019 000142", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive outer nuclear layer", "ONL Control rep3", "ONL Control rep3", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000142_S13_L001_R1_001.fastq.gz MCWR_2019_000142_S13_L001_R2_001.fastq.gz MCWR_2019_000142_S13_L002_R1_001.fastq.gz MCWR_2019_000142_S13_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 10611460744.0, 35241917.0, "MCWR 2019 000142 S13 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:2729659216;C:2572974863;G:2597112533;T:2711584081;N:130051", 150, 150, null, null, 2729659216, 2572974863, 2597112533, 2711584081, 130051, "SRX25421495", "SRS22081651", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95524, 0.95438, 0.08233, 0.08236, 0.76654, 0.76682, 0.41657, 0.41626, 151, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33322, "SRR29927556", "SRX25421494", "SRS22081650", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL Control rep2", "MCWR 2019 000141", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive outer nuclear layer", "ONL Control rep2", "ONL Control rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000141_S12_L001_R1_001.fastq.gz MCWR_2019_000141_S12_L001_R2_001.fastq.gz MCWR_2019_000141_S12_L002_R1_001.fastq.gz MCWR_2019_000141_S12_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 12296763008.0, 40838426.0, "MCWR 2019 000141 S12 L001 R1 001.fastq.gz", "0:150.55 1:150.55", "A:3157494503;C:2976873172;G:3025100891;T:3137136259;N:158183", 150, 150, null, null, 3157494503, 2976873172, 3025100891, 3137136259, 158183, "SRX25421494", "SRS22081650", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.9531, 0.95203, 0.08284, 0.08254, 0.76816, 0.76879, 0.40735, 0.41583, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33323, "SRR29927557", "SRX25421493", "SRS22081649", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "ONL Control rep1", "MCWR 2019 000140", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:ONL Control rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive outer nuclear layer", "ONL Control rep1", "ONL Control rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000140_S11_L001_R1_001.fastq.gz MCWR_2019_000140_S11_L001_R2_001.fastq.gz MCWR_2019_000140_S11_L002_R1_001.fastq.gz MCWR_2019_000140_S11_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 12797441059.0, 42498374.0, "MCWR 2019 000140 S11 L001 R1 001.fastq.gz", "0:150.56 1:150.56", "A:3214435348;C:3160301138;G:3218337754;T:3204200743;N:166076", 150, 150, null, null, 3214435348, 3160301138, 3218337754, 3204200743, 166076, "SRX25421493", "SRS22081649", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.95836, 0.95804, 0.0672, 0.06787, 0.79255, 0.7933, 0.37626, 0.37493, 149, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33324, "SRR29927558", "SRX25421492", "SRS22081648", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "GCL Control rep2", "MCWR 2019 000129", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive ganglion cell layer", "GCL Control rep2", "GCL Control rep2", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000129_S2_L001_R1_001.fastq.gz MCWR_2019_000129_S2_L001_R2_001.fastq.gz MCWR_2019_000129_S2_L002_R1_001.fastq.gz MCWR_2019_000129_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9904585990.0, 32898356.0, "MCWR 2019 000129 S2 L001 R1 001.fastq.gz", "0:150.53 1:150.54", "A:2686769990;C:2251531625;G:2320304039;T:2645855407;N:124929", 150, 150, null, null, 2686769990, 2251531625, 2320304039, 2645855407, 124929, "SRX25421492", "SRS22081648", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.93013, 0.93029, 0.10617, 0.10657, 0.74712, 0.74757, 0.56746, 0.56517, 150, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [33325, "SRR29927559", "SRX25421491", "SRS22081647", "SRP521592", "PRJNA1139127", "Laser capture microdissection RNA sequencing of zebrafish optic nerve regeneration", "PRJNA1139127", "Other", "Zebrafish have the ability to successfully regenerate the connection from the eye to the brain following optic nerve injury in adult. To identify differentially expressed genes in the affected tissues we performed laser capture mRNA sequencing of the retinal ganglion cell layer inner nuclear layer outer nuclear layer and bulk optic nerve in 3 day post optic nerve injury versus naive control animals. The 3 xxx post injury time point was chosen as a time when axons are actively regenerating throughout the optic nerve to the optic chiasm. These data provide a resource for identifying genes expressed in each tissue and their differential expression during optic nerve regeneration.", null, null, null, "GCL Control rep1", "MCWR 2019 000128", null, "strain:wild type|dev stage:adult|collection date:2019 10 18|geo loc name:USA: Wisconsin Milwaukee|sex:male|tissue:retina|treatment:GCL Control rep1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio: naive ganglion cell layer", "GCL Control rep1", "GCL Control rep1", "SMART Seqv4", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP521592", null, null, "MCWR_2019_000128_S1_L001_R1_001.fastq.gz MCWR_2019_000128_S1_L001_R2_001.fastq.gz MCWR_2019_000128_S1_L002_R1_001.fastq.gz MCWR_2019_000128_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 11199698460.0, 37200254.0, "MCWR 2019 000128 S1 L001 R1 001.fastq.gz", "0:150.53 1:150.53", "A:3065207886;C:2519670393;G:2596314938;T:3018365726;N:139517", 150, 150, null, null, 3065207886, 2519670393, 2596314938, 3018365726, 139517, "SRX25421491", "SRS22081647", "SRA1930690", "Medical College of Wisconsin|Cell Biology, Neurobiology, and Anatomy", "Medical College of Wisconsin", 2, 0.93213, 0.93206, 0.13073, 0.13125, 0.7305, 0.73079, 0.5518, 0.55133, 149, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2024-07-23", "Adult", "Adult", "Eye", "Sensory System"], [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. 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", "GSM8784928", "GSM8784928: FAC sorted RGCs at 6dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784928 r1", "GSM8784928", "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, "GC121312.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 375101328.0, 7354928.0, "GSM8784928 r1", "0:51", "A:98240052;C:88061621;G:89879822;T:98883790;N:36043", 51, null, null, null, 98240052, 88061621, 89879822, 98883790, 36043, "SRX27626961", "SRS24034228", "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"], [34834, "SRR32289956", "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. 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", "GSM8784928", "GSM8784928: FAC sorted RGCs at 6dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784928 r1", "GSM8784928", "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, "GC121312.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 382030290.0, 7490790.0, "GSM8784928 r2", "0:51", "A:100050525;C:89650775;G:91497813;T:100795370;N:35807", 51, null, null, null, 100050525, 89650775, 91497813, 100795370, 35807, "SRX27626961", "SRS24034228", "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"], [34835, "SRR32289957", "SRX27626960", "SRS24034231", "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 2", "GSM8784927", 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 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", "GSM8784927", "GSM8784927: FAC sorted RGCs at 6dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784927 r1", "GSM8784927", "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, "GC121311.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 359457486.0, 7048186.0, "GSM8784927 r1", "0:51", "A:94049871;C:84581283;G:86196196;T:94595815;N:34321", 51, null, null, null, 94049871, 84581283, 86196196, 94595815, 34321, "SRX27626960", "SRS24034231", "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"], [34836, "SRR32289958", "SRX27626960", "SRS24034231", "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 2", "GSM8784927", 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 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", "GSM8784927", "GSM8784927: FAC sorted RGCs at 6dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784927 r1", "GSM8784927", "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, "GC121311.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 368062155.0, 7216905.0, "GSM8784927 r2", "0:51", "A:96303888;C:86587511;G:88207050;T:96929121;N:34585", 51, null, null, null, 96303888, 86587511, 88207050, 96929121, 34585, "SRX27626960", "SRS24034231", "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"], [34837, "SRR32289959", "SRX27626959", "SRS24034229", "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 1", "GSM8784926", 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 6dpi 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", "GSM8784926", "GSM8784926: FAC sorted RGCs at 6dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784926 r1", "GSM8784926", "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, "GC121310.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 308100945.0, 6041195.0, "GSM8784926 r1", "0:51", "A:86887196;C:64730880;G:65880791;T:90571586;N:30492", 51, null, null, null, 86887196, 64730880, 65880791, 90571586, 30492, "SRX27626959", "SRS24034229", "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"], [34838, "SRR32289960", "SRX27626959", "SRS24034229", "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 1", "GSM8784926", 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 6dpi 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", "GSM8784926", "GSM8784926: FAC sorted RGCs at 6dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784926 r1", "GSM8784926", "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, "GC121310.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 318837465.0, 6251715.0, "GSM8784926 r2", "0:51", "A:89949594;C:66936819;G:68101167;T:93818871;N:31014", 51, null, null, null, 89949594, 66936819, 68101167, 93818871, 31014, "SRX27626959", "SRS24034229", "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"], [34839, "SRR32289961", "SRX27626958", "SRS24034226", "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 3dpi biological replicate 6", "GSM8784925", 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 3dpi 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", "GSM8784925", "GSM8784925: FAC sorted RGCs at 3dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784925 r1", "GSM8784925", "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, "GC122372.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 330289260.0, 6476260.0, "GSM8784925 r1", "0:51", "A:86654778;C:77586975;G:79218167;T:86799619;N:29721", 51, null, null, null, 86654778, 77586975, 79218167, 86799619, 29721, "SRX27626958", "SRS24034226", "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"], [34840, "SRR32289962", "SRX27626958", "SRS24034226", "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 3dpi biological replicate 6", "GSM8784925", 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 3dpi 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", "GSM8784925", "GSM8784925: FAC sorted RGCs at 3dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784925 r1", "GSM8784925", "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, "GC122372.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 337840524.0, 6624324.0, "GSM8784925 r2", "0:51", "A:88622074;C:79353340;G:80979292;T:88855871;N:29947", 51, null, null, null, 88622074, 79353340, 80979292, 88855871, 29947, "SRX27626958", "SRS24034226", "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"], [34841, "SRR32289963", "SRX27626957", "SRS24034227", "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 3dpi biological replicate 5", "GSM8784924", 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 3dpi 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", "GSM8784924", "GSM8784924: FAC sorted RGCs at 3dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784924 r1", "GSM8784924", "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, "GC122371.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 368108820.0, 7217820.0, "GSM8784924 r1", "0:51", "A:98464174;C:82788417;G:84631916;T:102188956;N:35357", 51, null, null, null, 98464174, 82788417, 84631916, 102188956, 35357, "SRX27626957", "SRS24034227", "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"]], "truncated": false, "filtered_table_rows_count": 195, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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