rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 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,,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,,,,,,,,,Raw reads: 48 HC1,webin reads 48 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1055463738,792073627,817607736,1103223790,73200,ERX13237628,ERS21098715,ERA30883416,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,58PR3 S26 R1 001.fastq.gz,58 PR3,,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,,,,,,,,,Raw reads: 58 PR3,webin reads 58 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 58 PR3,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,58PR3_S26_R1_001.fastq.gz,fastq,3869469736.0,38850717.0,webin reads 58 PR3,0:99.60,A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717,99,,,,1103909449,804146524,827344036,1134036010,33717,ERX13237717,ERS21098721,ERA30883529,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System 19089,ERR13835010,ERX13237776,ERS21098726,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,,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,,,,,,,,,Raw reads: 58 AC4,webin reads 58 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1038047870,736262498,759315202,1073962987,60094,ERX13237776,ERS21098726,ERA30883721,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,48PR2 S13 R1 001.fastq.gz,48 PR2,,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,,,,,,,,,Raw reads: 48 PR2,webin reads 48 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,ERP164534,Raw reads: 48 PR2,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,48PR2_S13_R1_001.fastq.gz,fastq,3809299607.0,38404185.0,webin reads 48 PR2,0:99.19,A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777,99,,,,1067728192,802585802,828435932,1110435904,113777,ERX13225546,ERS21098708,ERA30879682,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System 19091,ERR13834854,ERX13237620,ERS21098714,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. 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,,retinal neurons,48AC4 S19 R1 001.fastq.gz,48 AC4,,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,,,,,,,,,Raw reads: 48 AC4,webin reads 48 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,966160063,707754156,733039262,1003772756,75657,ERX13237620,ERS21098714,ERA30883390,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,48PR4 S15 R1 001.fastq.gz,48 PR4,,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,,,,,,,,,Raw reads: 48 PR4,webin reads 48 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1214448497,927512154,957491418,1266385355,106503,ERX13231590,ERS21098710,ERA30883309,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,58AC1 S28 R1 001.fastq.gz,58 AC1,,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,,,,,,,,,Raw reads: 58 AC1,webin reads 58 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1060419097,761984557,786533722,1101603428,227465,ERX13237759,ERS21098723,ERA30883659,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,Hatching,Embryo,Eye,Sensory System 19094,ERR13834875,ERX13237641,ERS21098717,ERP164534,PRJEB80557,RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf,e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed,Other,This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol.,ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01,,retinal neurons,48HC3 S22 R1 001.fastq.gz,48 HC3,,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,,,,,,,,,Raw reads: 48 HC3,webin reads 48 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,856250957,655140994,677078911,894558582,49142,ERX13237641,ERS21098717,ERA30883447,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,58PR2 S25 R1 001.fastq.gz,58 PR2,,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,,,,,,,,,Raw reads: 58 PR2,webin reads 58 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1089593011,803322469,827777017,1128836774,42547,ERX13237665,ERS21098720,ERA30883518,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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. 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,,retinal neurons,58PR1 S24 R1 001.fastq.gz,58 PR1,,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,,,,,,,,,Raw reads: 58 PR1,webin reads 58 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1135075173,807489123,827964380,1175109762,32802,ERX13237655,ERS21098719,ERA30883497,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,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,,,,,,,,,Raw reads: 58 HC2,webin reads 58 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1070592288,757099665,780689044,1102575310,280762,ERX13237785,ERS21098728,ERA30883748,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38PR2 S2 R1 001.fastq.gz,38 PR2,,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,,,,,,,,,Raw reads: 38 PR2,webin reads 38 PR2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,969862466,733798241,755135957,1004440555,43890,ERX13224862,ERS21098697,ERA30879238,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38HC3 S11 R1 001.fastq.gz,38 HC3,,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,,,,,,,,,Raw reads: 38 HC3,webin reads 38 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1222778761,918257887,948838973,1270939370,106882,ERX13225536,ERS21098706,ERA30879613,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,48AC2 S17 R1 001.fastq.gz,48 AC2,,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,,,,,,,,,Raw reads: 48 AC2,webin reads 48 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,902438127,672433401,694813369,935445436,76255,ERX13231602,ERS21098712,ERA30883343,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58AC3 S30 R1 001.fastq.gz,58 AC3,,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,,,,,,,,,Raw reads: 58 AC3,webin reads 58 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1080745150,779903026,803258485,1118994941,91531,ERX13237770,ERS21098725,ERA30883697,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,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,,,,,,,,,Raw reads: 48 HC2,webin reads 48 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,959488173,721171249,745705870,997922014,60559,ERX13237634,ERS21098716,ERA30883434,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,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,,,,,,,,,Raw reads: 38 HC1,webin reads 38 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1064199311,791310791,818910597,1110118632,102167,ERX13224949,ERS21098704,ERA30879548,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,48HC4 S23 R1 001.fastq.gz,48 HC4,,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,,,,,,,,,Raw reads: 48 HC4,webin reads 48 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1035049987,763030378,788062167,1074303516,228267,ERX13237646,ERS21098718,ERA30883470,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,48PR3 S14 R1 001.fastq.gz,48 PR3,,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,,,,,,,,,Raw reads: 48 PR3,webin reads 48 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1195251409,889346003,917240118,1230272855,60079,ERX13225633,ERS21098709,ERA30879704,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,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,,,,,,,,,Raw reads: 38 AC1,webin reads 38 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1066720805,818958589,843762182,1107403844,75693,ERX13224883,ERS21098700,ERA30879356,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38AC3 S7 R1 001.fastq.gz,38 AC3,,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,,,,,,,,,Raw reads: 38 AC3,webin reads 38 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,970868997,726795179,750560378,1004408693,74130,ERX13224895,ERS21098702,ERA30879451,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,48AC3 S18 R1 001.fastq.gz,48 AC3,,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,,,,,,,,,Raw reads: 48 AC3,webin reads 48 AC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1047204450,786943605,812327274,1086893109,260473,ERX13234350,ERS21098713,ERA30883366,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38AC4 S8 R1 001.fastq.gz,38 AC4,,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,,,,,,,,,Raw reads: 38 AC4,webin reads 38 AC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1156746387,877063962,905379690,1191264308,175277,ERX13224905,ERS21098703,ERA30879532,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38HC2 S10 R1 001.fastq.gz,38 HC2,,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,,,,,,,,,Raw reads: 38 HC2,webin reads 38 HC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1195817135,879958039,908085464,1237394738,84761,ERX13224953,ERS21098705,ERA30879582,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,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,,,,,,,,,Raw reads: 38 PR3,webin reads 38 PR3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1093221995,818047738,843661747,1138957138,121488,ERX13224866,ERS21098698,ERA30879273,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38AC2 S6 R1 001.fastq.gz,38 AC2,,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,,,,,,,,,Raw reads: 38 AC2,webin reads 38 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1089960083,827936673,855955684,1139372607,117960,ERX13224887,ERS21098701,ERA30879382,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58HC4 S35 R1 001.fastq.gz,58 HC4,,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,,,,,,,,,Raw reads: 58 HC4,webin reads 58 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1255080581,916490847,946212615,1300735054,36918,ERX13237798,ERS21098730,ERA30883773,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,48AC1 S16 R1 001.fastq.gz,48 AC1,,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,,,,,,,,,Raw reads: 48 AC1,webin reads 48 AC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1105258159,824538054,854253688,1149538152,81068,ERX13231595,ERS21098711,ERA30883326,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38PR1 S1 R1 001.fastq.gz,38 PR1,,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,,,,,,,,,Raw reads: 38 PR1,webin reads 38 PR1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1193880575,899261652,926114030,1236860186,41845,ERX13224851,ERS21098696,ERA30879152,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38PR4 S4 R1 001.fastq.gz,38 PR4,,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,,,,,,,,,Raw reads: 38 PR4,webin reads 38 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1043231302,789255840,812957881,1080801843,61180,ERX13224871,ERS21098699,ERA30879302,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58HC3 S34 R1 001.fastq.gz,58 HC3,,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,,,,,,,,,Raw reads: 58 HC3,webin reads 58 HC3,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1012516999,723225071,745152410,1042976092,28640,ERX13237791,ERS21098729,ERA30883757,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58HC1 S32 R1 001.fastq.gz,58 HC1,,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,,,,,,,,,Raw reads: 58 HC1,webin reads 58 HC1,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,980894291,707196785,729948858,1018400124,53763,ERX13237780,ERS21098727,ERA30883731,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58PR4 S27 R1 001.fastq.gz,58 PR4,,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,,,,,,,,,Raw reads: 58 PR4,webin reads 58 PR4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,875776938,633951750,653308475,905949639,54012,ERX13237753,ERS21098722,ERA30883641,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,38HC4 S12 R1 001.fastq.gz,38 HC4,,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,,,,,,,,,Raw reads: 38 HC4,webin reads 38 HC4,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,939537209,709367668,731849729,973193819,46015,ERX13225540,ERS21098707,ERA30879650,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,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,,retinal neurons,58AC2 S29 R1 001.fastq.gz,58 AC2,,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,,,,,,,,,Raw reads: 58 AC2,webin reads 58 AC2,,,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq X,,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,,,,1111663794,793747086,817730996,1148980297,39918,ERX13237763,ERS21098724,ERA30883678,Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive,Gulbenkian Institute for Molecular Medicine,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_plate,smartseq,,Belgium,2025-01-01,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.,,,,FAC sorted RGCs at 14dpi biological replicate 6,GSM8784941,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,121395551,104372745,106322577,123006247,42894,SRX27626974,SRS24034243,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 6,GSM8784941,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,124363664,106868642,108780226,126189949,43599,SRX27626974,SRS24034243,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 5,GSM8784940,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,119318402,105882527,107813042,120365525,43093,SRX27626973,SRS24034241,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 5,GSM8784940,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,122313464,108440796,110356081,123457974,43725,SRX27626973,SRS24034241,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 4,GSM8784939,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104203040,94204942,95935068,104813749,37694,SRX27626972,SRS24034242,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 4,GSM8784939,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,106355289,96099106,97825197,107096823,38360,SRX27626972,SRS24034242,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 3,GSM8784938,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104716428,90712029,92875673,105476998,37914,SRX27626971,SRS24034240,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 3,GSM8784938,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,107484459,93060010,95238340,108369497,38759,SRX27626971,SRS24034240,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 2,GSM8784937,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,107517102,84333044,85962742,109191597,38289,SRX27626970,SRS24034239,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 2,GSM8784937,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,111048661,86998697,88636677,112933522,39455,SRX27626970,SRS24034239,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 1,GSM8784936,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,101071342,75109849,76553150,105519857,35082,SRX27626969,SRS24034236,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 14dpi biological replicate 1,GSM8784936,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104421674,77537410,79038293,109169570,35678,SRX27626969,SRS24034236,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 5,GSM8784935,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104505636,95925686,97605050,105285164,37770,SRX27626968,SRS24034237,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 5,GSM8784935,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,106698116,97949900,99548706,107586633,37769,SRX27626968,SRS24034237,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 4,GSM8784934,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,83667318,75715675,77201096,84031268,30058,SRX27626967,SRS24034233,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 4,GSM8784934,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,85253239,77113202,78588132,85671193,30203,SRX27626967,SRS24034233,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 3,GSM8784933,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,100725108,90120177,92143732,100747122,36413,SRX27626966,SRS24034235,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 3,GSM8784933,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,102939588,92028680,94033209,103058157,36373,SRX27626966,SRS24034235,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 2,GSM8784932,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,103913407,93411140,95295922,104041015,37732,SRX27626965,SRS24034238,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 2,GSM8784932,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,106734482,95879695,97797451,106984011,38057,SRX27626965,SRS24034238,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 1,GSM8784931,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,100707954,76739501,77474055,102464781,34561,SRX27626964,SRS24034232,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 10dpi biological replicate 1,GSM8784931,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104043292,79231475,79962686,105999425,35303,SRX27626964,SRS24034232,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 5,GSM8784930,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,101986811,88337442,89758931,103581971,35946,SRX27626963,SRS24034234,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 5,GSM8784930,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104937168,90871625,92274823,106726849,36890,SRX27626963,SRS24034234,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 4,GSM8784929,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,102962865,94382913,96076584,103896489,38418,SRX27626962,SRS24034230,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 4,GSM8784929,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,105635966,96802890,98458161,106705494,38806,SRX27626962,SRS24034230,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 3,GSM8784928,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,98240052,88061621,89879822,98883790,36043,SRX27626961,SRS24034228,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 3,GSM8784928,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,100050525,89650775,91497813,100795370,35807,SRX27626961,SRS24034228,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 2,GSM8784927,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,94049871,84581283,86196196,94595815,34321,SRX27626960,SRS24034231,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 2,GSM8784927,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,96303888,86587511,88207050,96929121,34585,SRX27626960,SRS24034231,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 1,GSM8784926,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,86887196,64730880,65880791,90571586,30492,SRX27626959,SRS24034229,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 6dpi biological replicate 1,GSM8784926,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,89949594,66936819,68101167,93818871,31014,SRX27626959,SRS24034229,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 6,GSM8784925,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,86654778,77586975,79218167,86799619,29721,SRX27626958,SRS24034226,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 6,GSM8784925,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,88622074,79353340,80979292,88855871,29947,SRX27626958,SRS24034226,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 5,GSM8784924,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,98464174,82788417,84631916,102188956,35357,SRX27626957,SRS24034227,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 5,GSM8784924,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,101126361,85046503,86891002,105168387,36022,SRX27626957,SRS24034227,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 4,GSM8784923,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,73208995,69469968,70853373,72949032,28064,SRX27626956,SRS24034225,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 4,GSM8784923,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,75131024,71285864,72635665,74893973,28337,SRX27626956,SRS24034225,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 3,GSM8784922,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,93438522,84870850,86529862,93916370,33629,SRX27626955,SRS24034223,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 3,GSM8784922,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,95070256,86325431,87987533,95608156,33882,SRX27626955,SRS24034223,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 2,GSM8784921,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,101960329,92790371,94697001,102022049,36952,SRX27626954,SRS24034224,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 2,GSM8784921,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104424027,95011852,96926223,104627136,37634,SRX27626954,SRS24034224,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 1,GSM8784920,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,93114431,74857016,76108927,94907017,33783,SRX27626953,SRS24034222,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 3dpi biological replicate 1,GSM8784920,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,97070049,77993850,79259723,99025646,34628,SRX27626953,SRS24034222,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 1dpi biological replicate 7,GSM8784919,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,104916639,90350948,92325077,106392449,36756,SRX27626952,SRS24034220,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 1dpi biological replicate 7,GSM8784919,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,107284622,92356101,94308190,108850087,36893,SRX27626952,SRS24034220,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 1dpi biological replicate 6,GSM8784918,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,92193678,70679080,72151366,96339266,30836,SRX27626951,SRS24034221,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 1dpi biological replicate 6,GSM8784918,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,94891966,72728396,74206983,99364490,31009,SRX27626951,SRS24034221,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,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.,,,,FAC sorted RGCs at 1dpi biological replicate 5,GSM8784917,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,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,,,,88455336,66904117,68494022,94878199,30362,SRX27626950,SRS24034218,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34856,SRR32289978,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.,,,,FAC sorted RGCs at 1dpi biological replicate 5,GSM8784917,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC122367.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,327003024.0,6411824.0,GSM8784917 r2,0:51,A:90712200;C:68607337;G:70232257;T:97420994;N:30236,51,,,,90712200,68607337,70232257,97420994,30236,SRX27626950,SRS24034218,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34857,SRR32289979,SRX27626949,SRS24034219,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.,,,,FAC sorted RGCs at 1dpi biological replicate 4,GSM8784916,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784916,GSM8784916: FAC sorted RGCs at 1dpi biological replicate 4; Danio rerio; RNA Seq,GSM8784916 r1,GSM8784916,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121301.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,387759885.0,7603135.0,GSM8784916 r1,0:51,A:102783169;C:88945135;G:91353292;T:104641521;N:36768,51,,,,102783169,88945135,91353292,104641521,36768,SRX27626949,SRS24034219,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34858,SRR32289980,SRX27626949,SRS24034219,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.,,,,FAC sorted RGCs at 1dpi biological replicate 4,GSM8784916,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784916,GSM8784916: FAC sorted RGCs at 1dpi biological replicate 4; Danio rerio; RNA Seq,GSM8784916 r1,GSM8784916,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121301.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,397404189.0,7792239.0,GSM8784916 r2,0:51,A:105304214;C:91200661;G:93584392;T:107277465;N:37457,51,,,,105304214,91200661,93584392,107277465,37457,SRX27626949,SRS24034219,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34859,SRR32289981,SRX27626948,SRS24034216,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.,,,,FAC sorted RGCs at 1dpi biological replicate 3,GSM8784915,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784915,GSM8784915: FAC sorted RGCs at 1dpi biological replicate 3; Danio rerio; RNA Seq,GSM8784915 r1,GSM8784915,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121300.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,428248785.0,8397035.0,GSM8784915 r1,0:51,A:112023158;C:100515159;G:102620937;T:113048752;N:40779,51,,,,112023158,100515159,102620937,113048752,40779,SRX27626948,SRS24034216,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34860,SRR32289982,SRX27626948,SRS24034216,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.,,,,FAC sorted RGCs at 1dpi biological replicate 3,GSM8784915,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784915,GSM8784915: FAC sorted RGCs at 1dpi biological replicate 3; Danio rerio; RNA Seq,GSM8784915 r1,GSM8784915,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121300.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,437907063.0,8586413.0,GSM8784915 r2,0:51,A:114573702;C:102734144;G:104841829;T:115716348;N:41040,51,,,,114573702,102734144,104841829,115716348,41040,SRX27626948,SRS24034216,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34861,SRR32289983,SRX27626947,SRS24034217,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.,,,,FAC sorted RGCs at 1dpi biological replicate 2,GSM8784914,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784914,GSM8784914: FAC sorted RGCs at 1dpi biological replicate 2; Danio rerio; RNA Seq,GSM8784914 r1,GSM8784914,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121299.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,402924888.0,7900488.0,GSM8784914 r1,0:51,A:107947778;C:91046861;G:93204506;T:110687203;N:38540,51,,,,107947778,91046861,93204506,110687203,38540,SRX27626947,SRS24034217,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34862,SRR32289984,SRX27626947,SRS24034217,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.,,,,FAC sorted RGCs at 1dpi biological replicate 2,GSM8784914,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 2,GSM8784914,GSM8784914: FAC sorted RGCs at 1dpi biological replicate 2; Danio rerio; RNA Seq,GSM8784914 r1,GSM8784914,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121299.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,413979393.0,8117243.0,GSM8784914 r2,0:51,A:110924319;C:93515017;G:95646686;T:113854113;N:39258,51,,,,110924319,93515017,95646686,113854113,39258,SRX27626947,SRS24034217,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34863,SRR32289985,SRX27626946,SRS24034215,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.,,,,FAC sorted RGCs at 1dpi biological replicate 1,GSM8784913,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1,GSM8784913,GSM8784913: FAC sorted RGCs at 1dpi biological replicate 1; Danio rerio; RNA Seq,GSM8784913 r1,GSM8784913,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121298.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,360875541.0,7075991.0,GSM8784913 r1,0:51,A:102005383;C:74767685;G:76535877;T:107531326;N:35270,51,,,,102005383,74767685,76535877,107531326,35270,SRX27626946,SRS24034215,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34864,SRR32289986,SRX27626946,SRS24034215,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.,,,,FAC sorted RGCs at 1dpi biological replicate 1,GSM8784913,,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 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:optic nerve crush|batch:RNA extraction batch 1,GSM8784913,GSM8784913: FAC sorted RGCs at 1dpi biological replicate 1; Danio rerio; RNA Seq,GSM8784913 r1,GSM8784913,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121298.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,372258078.0,7299178.0,GSM8784913 r2,0:51,A:105213098;C:77053267;G:78863209;T:111092762;N:35742,51,,,,105213098,77053267,78863209,111092762,35742,SRX27626946,SRS24034215,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34865,SRR32289987,SRX27626945,SRS24034212,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.,,,,FAC sorted RGCs at naive condition biological replicate 6,GSM8784912,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784912,GSM8784912: FAC sorted RGCs at naive condition biological replicate 6; Danio rerio; RNA Seq,GSM8784912 r1,GSM8784912,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121295.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,304489992.0,5970392.0,GSM8784912 r1,0:51,A:82425732;C:67909372;G:69611868;T:84514015;N:29005,51,,,,82425732,67909372,69611868,84514015,29005,SRX27626945,SRS24034212,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34866,SRR32289988,SRX27626945,SRS24034212,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.,,,,FAC sorted RGCs at naive condition biological replicate 6,GSM8784912,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784912,GSM8784912: FAC sorted RGCs at naive condition biological replicate 6; Danio rerio; RNA Seq,GSM8784912 r1,GSM8784912,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121295.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,311693232.0,6111632.0,GSM8784912 r2,0:51,A:84387116;C:69487428;G:71190724;T:86598688;N:29276,51,,,,84387116,69487428,71190724,86598688,29276,SRX27626945,SRS24034212,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34867,SRR32289989,SRX27626944,SRS24034214,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.,,,,FAC sorted RGCs at naive condition biological replicate 5,GSM8784911,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784911,GSM8784911: FAC sorted RGCs at naive condition biological replicate 5; Danio rerio; RNA Seq,GSM8784911 r1,GSM8784911,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121294.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,371909136.0,7292336.0,GSM8784911 r1,0:51,A:97343920;C:87664048;G:89481936;T:97384353;N:34879,51,,,,97343920,87664048,89481936,97384353,34879,SRX27626944,SRS24034214,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34868,SRR32289990,SRX27626944,SRS24034214,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.,,,,FAC sorted RGCs at naive condition biological replicate 5,GSM8784911,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784911,GSM8784911: FAC sorted RGCs at naive condition biological replicate 5; Danio rerio; RNA Seq,GSM8784911 r1,GSM8784911,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121294.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,379291284.0,7437084.0,GSM8784911 r2,0:51,A:99243449;C:89397613;G:91207377;T:99407666;N:35179,51,,,,99243449,89397613,91207377,99407666,35179,SRX27626944,SRS24034214,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34869,SRR32289991,SRX27626943,SRS24034213,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.,,,,FAC sorted RGCs at naive condition biological replicate 4,GSM8784910,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784910,GSM8784910: FAC sorted RGCs at naive condition biological replicate 4; Danio rerio; RNA Seq,GSM8784910 r1,GSM8784910,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121293.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,381808797.0,7486447.0,GSM8784910 r1,0:51,A:102345832;C:86993840;G:89121190;T:103311576;N:36359,51,,,,102345832,86993840,89121190,103311576,36359,SRX27626943,SRS24034213,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34870,SRR32289992,SRX27626943,SRS24034213,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.,,,,FAC sorted RGCs at naive condition biological replicate 4,GSM8784910,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 2,GSM8784910,GSM8784910: FAC sorted RGCs at naive condition biological replicate 4; Danio rerio; RNA Seq,GSM8784910 r1,GSM8784910,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121293.220715.HiSeq4000.FCB.lane7.gcap_18_12.R1.fastq.gz,fastq,392824899.0,7702449.0,GSM8784910 r2,0:51,A:105300909;C:89459531;G:91629489;T:106397902;N:37068,51,,,,105300909,89459531,91629489,106397902,37068,SRX27626943,SRS24034213,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System 34871,SRR32289993,SRX27626942,SRS24034211,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.,,,,FAC sorted RGCs at naive condition biological replicate 3,GSM8784909,,tissue:Retinal ganglion cells|cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1|geo loc name:missing|collection date:missing,FAC sorted RGCs at naive condition 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,,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,,cell type:Retinal ganglion cells|genotype:Tgisl2b:eGFPzc7Tg|treatment:Non injured|batch:RNA extraction batch 1,GSM8784909,GSM8784909: FAC sorted RGCs at naive condition biological replicate 3; Danio rerio; RNA Seq,GSM8784909 r1,GSM8784909,1,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP562853,,,GC121292.220715.HiSeq4000.FCB.lane6.gcap_18_12.R1.fastq.gz,fastq,319281267.0,6260417.0,GSM8784909 r1,0:51,A:89536872;C:68243564;G:69702232;T:91767357;N:31242,51,,,,89536872,68243564,69702232,91767357,31242,SRX27626942,SRS24034211,SRA2075201,KU Leuven,KU Leuven,,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,Belgium,2025-02-10,Undetermined,Adult,Eye,Sensory System