{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\" 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", "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. 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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", "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"], [25107, "SRR25605432", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 21603309774.0, 156545723.0, "GSM7702835 r1", "0:10 1:10 2:28 3:90", "A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216", 10, 10, 28, 90, 3960451458, 3105338977, 3480072824, 3541218595, 2033216, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94286, null, 0.14175, null, 0.78395, null, 0.51541, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25108, "SRR25605433", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 22413465270.0, 162416415.0, "GSM7702835 r2", "0:10 1:10 2:28 3:90", "A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021", 10, 10, 28, 90, 4104405257, 3220235633, 3625448968, 3667329471, 58021, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94239, null, 0.14234, null, 0.78338, null, 0.50616, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25109, "SRR25822232", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz", "fastq fastq fastq fastq", 21424338264.0, 155248828.0, "GSM7702835 r3", "0:10 1:10 2:28 3:90", "A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932", 10, 10, 28, 90, 3928077020, 3077672525, 3451667186, 3513734857, 1242932, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.9433, null, 0.14242, null, 0.78328, null, 0.52384, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25110, "SRR25822233", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 22542479952.0, 163351304.0, "GSM7702835 r4", "0:10 1:10 2:28 3:90", "A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485", 10, 10, 28, 90, 4130174287, 3235362228, 3643457599, 3691295761, 1327485, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94183, null, 0.14124, null, 0.78301, null, 0.50517, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25111, "SRR25605434", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 20161522758.0, 146097991.0, "GSM7702834 r1", "0:10 1:10 2:28 3:90", "A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112", 10, 10, 28, 90, 3649819934, 2958286158, 3267504300, 3271384686, 1824112, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94851, null, 0.1483, null, 0.80012, null, 0.52549, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25112, "SRR25605435", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 20708273928.0, 150059956.0, "GSM7702834 r2", "0:10 1:10 2:28 3:90", "A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351", 10, 10, 28, 90, 3746088654, 3037032642, 3368938151, 3353289242, 47351, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94778, null, 0.14581, null, 0.80028, null, 0.52885, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25113, "SRR25822230", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz", "fastq fastq fastq fastq", 20078121078.0, 145493631.0, "GSM7702834 r3", "0:10 1:10 2:28 3:90", "A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962", 10, 10, 28, 90, 3634984131, 2943891505, 3255149272, 3259243920, 1157962, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94884, null, 0.14622, null, 0.80099, null, 0.52572, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25114, "SRR25822231", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 20884392978.0, 151336181.0, "GSM7702834 r4", "0:10 1:10 2:28 3:90", "A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970", 10, 10, 28, 90, 3779370721, 3059502508, 3396295214, 3383865877, 1221970, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94896, null, 0.14559, null, 0.8002, null, 0.51418, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25115, "SRR25605436", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py|options: allowEarlyFileEnd", "1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 22174775364.0, 160686778.0, "GSM7702833 r1", "0:10 1:10 2:28 3:90", "A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885", 10, 10, 28, 90, 4207510387, 3050740898, 3362227609, 3839333241, 1997885, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93287, null, 0.11844, null, 0.81087, null, 0.55264, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25116, "SRR25605437", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py|options: allowEarlyFileEnd", "1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 22047847518.0, 159767011.0, "GSM7702833 r2", "0:10 1:10 2:28 3:90", "A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001", 10, 10, 28, 90, 4174013532, 3033959926, 3357962867, 3813042664, 52001, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93359, null, 0.11585, null, 0.81087, null, 0.55705, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25117, "SRR25822228", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz", "fastq fastq fastq fastq", 22010894568.0, 159499236.0, "GSM7702833 r3", "0:10 1:10 2:28 3:90", "A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918", 10, 10, 28, 90, 4176090595, 3026940106, 3336506731, 3814128890, 1264918, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93457, null, 0.11733, null, 0.81032, null, 0.55203, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25118, "SRR25822229", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 22227220746.0, 161066817.0, "GSM7702833 r4", "0:10 1:10 2:28 3:90", "A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858", 10, 10, 28, 90, 4209198596, 3055507768, 3382717459, 3847294849, 1294858, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93428, null, 0.11629, null, 0.81014, null, 0.56014, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25119, "SRR25605438", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 25141955454.0, 182188083.0, "GSM7702832 r1", "0:10 1:10 2:28 3:90", "A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244", 10, 10, 28, 90, 4942067104, 3446689328, 3778138998, 4227670796, 2361244, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90803, null, 0.11273, null, 0.81872, null, 0.54345, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25120, "SRR25605439", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz", "fastq fastq fastq fastq", 25433730786.0, 184302397.0, "GSM7702832 r2", "0:10 1:10 2:28 3:90", "A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122", 10, 10, 28, 90, 4980326106, 3488986366, 3842594871, 4275245265, 63122, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.91035, null, 0.11175, null, 0.82016, null, 0.52814, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25121, "SRR25822226", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz", "fastq fastq fastq fastq", 24834656088.0, 179961276.0, "GSM7702832 r3", "0:10 1:10 2:28 3:90", "A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685", 10, 10, 28, 90, 4878672093, 3403443000, 3732878174, 4180051888, 1469685, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90776, null, 0.11325, null, 0.81852, null, 0.54011, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25122, "SRR25822227", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes \u2265 500 library size \u2265 800 and mitochondrial reads \u2264 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al. 2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes and other known genes for each cell type using information from the literature and ZFIN Sprague et al. 2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files matrix files Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 25609437216.0, 185575632.0, "GSM7702832 r4", "0:10 1:10 2:28 3:90", "A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424", 10, 10, 28, 90, 5015380345, 3509305882, 3867598814, 4308011415, 1510424, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90907, null, 0.11192, null, 0.81994, null, 0.50902, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "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"], [34842, "SRR32289964", "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.lane7.gcap_18_12.R1.fastq.gz", "fastq", 378268275.0, 7417025.0, "GSM8784924 r2", "0:51", "A:101126361;C:85046503;G:86891002;T:105168387;N:36022", 51, null, null, null, 101126361, 85046503, 86891002, 105168387, 36022, "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"], [34843, "SRR32289965", "SRX27626956", "SRS24034225", "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 4", "GSM8784923", 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 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", "GSM8784923", "GSM8784923: FAC sorted RGCs at 3dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784923 r1", "GSM8784923", "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, "GC121307.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 286509432.0, 5617832.0, "GSM8784923 r1", "0:51", "A:73208995;C:69469968;G:70853373;T:72949032;N:28064", 51, null, null, null, 73208995, 69469968, 70853373, 72949032, 28064, "SRX27626956", "SRS24034225", "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"], [34844, "SRR32289966", "SRX27626956", "SRS24034225", "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 4", "GSM8784923", 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 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", "GSM8784923", "GSM8784923: FAC sorted RGCs at 3dpi biological replicate 4; Danio rerio; RNA Seq", "GSM8784923 r1", "GSM8784923", "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, "GC121307.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 293974863.0, 5764213.0, "GSM8784923 r2", "0:51", "A:75131024;C:71285864;G:72635665;T:74893973;N:28337", 51, null, null, null, 75131024, 71285864, 72635665, 74893973, 28337, "SRX27626956", "SRS24034225", "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"], [34845, "SRR32289967", "SRX27626955", "SRS24034223", "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 3", "GSM8784922", 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 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", "GSM8784922", "GSM8784922: FAC sorted RGCs at 3dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784922 r1", "GSM8784922", "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, "GC121306.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 358789233.0, 7035083.0, "GSM8784922 r1", "0:51", "A:93438522;C:84870850;G:86529862;T:93916370;N:33629", 51, null, null, null, 93438522, 84870850, 86529862, 93916370, 33629, "SRX27626955", "SRS24034223", "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"], [34846, "SRR32289968", "SRX27626955", "SRS24034223", "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 3", "GSM8784922", 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 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", "GSM8784922", "GSM8784922: FAC sorted RGCs at 3dpi biological replicate 3; Danio rerio; RNA Seq", "GSM8784922 r1", "GSM8784922", "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, "GC121306.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 365025258.0, 7157358.0, "GSM8784922 r2", "0:51", "A:95070256;C:86325431;G:87987533;T:95608156;N:33882", 51, null, null, null, 95070256, 86325431, 87987533, 95608156, 33882, "SRX27626955", "SRS24034223", "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"], [34847, "SRR32289969", "SRX27626954", "SRS24034224", "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 2", "GSM8784921", 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 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", "GSM8784921", "GSM8784921: FAC sorted RGCs at 3dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784921 r1", "GSM8784921", "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, "GC121305.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 391506702.0, 7676602.0, "GSM8784921 r1", "0:51", "A:101960329;C:92790371;G:94697001;T:102022049;N:36952", 51, null, null, null, 101960329, 92790371, 94697001, 102022049, 36952, "SRX27626954", "SRS24034224", "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"], [34848, "SRR32289970", "SRX27626954", "SRS24034224", "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 2", "GSM8784921", 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 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", "GSM8784921", "GSM8784921: FAC sorted RGCs at 3dpi biological replicate 2; Danio rerio; RNA Seq", "GSM8784921 r1", "GSM8784921", "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, "GC121305.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 401026872.0, 7863272.0, "GSM8784921 r2", "0:51", "A:104424027;C:95011852;G:96926223;T:104627136;N:37634", 51, null, null, null, 104424027, 95011852, 96926223, 104627136, 37634, "SRX27626954", "SRS24034224", "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"], [34849, "SRR32289971", "SRX27626953", "SRS24034222", "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 1", "GSM8784920", 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 3dpi 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", "GSM8784920", "GSM8784920: FAC sorted RGCs at 3dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784920 r1", "GSM8784920", "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, "GC121304.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 339021174.0, 6647474.0, "GSM8784920 r1", "0:51", "A:93114431;C:74857016;G:76108927;T:94907017;N:33783", 51, null, null, null, 93114431, 74857016, 76108927, 94907017, 33783, "SRX27626953", "SRS24034222", "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"], [34850, "SRR32289972", "SRX27626953", "SRS24034222", "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 1", "GSM8784920", 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 3dpi 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", "GSM8784920", "GSM8784920: FAC sorted RGCs at 3dpi biological replicate 1; Danio rerio; RNA Seq", "GSM8784920 r1", "GSM8784920", "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, "GC121304.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 353383896.0, 6929096.0, "GSM8784920 r2", "0:51", "A:97070049;C:77993850;G:79259723;T:99025646;N:34628", 51, null, null, null, 97070049, 77993850, 79259723, 99025646, 34628, "SRX27626953", "SRS24034222", "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"], [34851, "SRR32289973", "SRX27626952", "SRS24034220", "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 1dpi biological replicate 7", "GSM8784919", 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 1dpi biological replicate 7", "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", "GSM8784919", "GSM8784919: FAC sorted RGCs at 1dpi biological replicate 7; Danio rerio; RNA Seq", "GSM8784919 r1", "GSM8784919", "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, "GC122370.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 394021869.0, 7725919.0, "GSM8784919 r1", "0:51", "A:104916639;C:90350948;G:92325077;T:106392449;N:36756", 51, null, null, null, 104916639, 90350948, 92325077, 106392449, 36756, "SRX27626952", "SRS24034220", "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"], [34852, "SRR32289974", "SRX27626952", "SRS24034220", "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 1dpi biological replicate 7", "GSM8784919", 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 1dpi biological replicate 7", "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", "GSM8784919", "GSM8784919: FAC sorted RGCs at 1dpi biological replicate 7; Danio rerio; RNA Seq", "GSM8784919 r1", "GSM8784919", "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, "GC122370.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 402835893.0, 7898743.0, "GSM8784919 r2", "0:51", "A:107284622;C:92356101;G:94308190;T:108850087;N:36893", 51, null, null, null, 107284622, 92356101, 94308190, 108850087, 36893, "SRX27626952", "SRS24034220", "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"], [34853, "SRR32289975", "SRX27626951", "SRS24034221", "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 1dpi biological replicate 6", "GSM8784918", 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 1dpi 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 1", "GSM8784918", "GSM8784918: FAC sorted RGCs at 1dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784918 r1", "GSM8784918", "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, "GC122368.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 331394226.0, 6497926.0, "GSM8784918 r1", "0:51", "A:92193678;C:70679080;G:72151366;T:96339266;N:30836", 51, null, null, null, 92193678, 70679080, 72151366, 96339266, 30836, "SRX27626951", "SRS24034221", "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"], [34854, "SRR32289976", "SRX27626951", "SRS24034221", "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 1dpi biological replicate 6", "GSM8784918", 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 1dpi 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 1", "GSM8784918", "GSM8784918: FAC sorted RGCs at 1dpi biological replicate 6; Danio rerio; RNA Seq", "GSM8784918 r1", "GSM8784918", "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, "GC122368.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz", "fastq", 341222844.0, 6690644.0, "GSM8784918 r2", "0:51", "A:94891966;C:72728396;G:74206983;T:99364490;N:31009", 51, null, null, null, 94891966, 72728396, 74206983, 99364490, 31009, "SRX27626951", "SRS24034221", "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"], [34855, "SRR32289977", "SRX27626950", "SRS24034218", "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 1dpi biological replicate 5", "GSM8784917", 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 1dpi 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 1", "GSM8784917", "GSM8784917: FAC sorted RGCs at 1dpi biological replicate 5; Danio rerio; RNA Seq", "GSM8784917 r1", "GSM8784917", "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, "GC122367.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz", "fastq", 318762036.0, 6250236.0, "GSM8784917 r1", "0:51", "A:88455336;C:66904117;G:68494022;T:94878199;N:30362", 51, null, null, null, 88455336, 66904117, 68494022, 94878199, 30362, "SRX27626950", "SRS24034218", "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": 555, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", 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