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555 rows where experiment.library_layout = "SINGLE" and tissue_curation = "Eye"

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devstage_curation 7

technology 5

experiment.library_selection 5

devstage_curation_coarse 5

experiment.platform 3

experiment.library_strategy 2

experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

  • Eye · 555 ✖

experiment.library_layout 1

  • SINGLE · 555 ✖
Link 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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
25107 25107 SRR25605432 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz fastq fastq fastq fastq 21603309774.0 156545723.0 GSM7702835 r1 0:10 1:10 2:28 3:90 A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216 10 10 28 90 3960451458 3105338977 3480072824 3541218595 2033216 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94286   0.14175   0.78395   0.51541   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25108 25108 SRR25605433 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz fastq fastq fastq fastq 22413465270.0 162416415.0 GSM7702835 r2 0:10 1:10 2:28 3:90 A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021 10 10 28 90 4104405257 3220235633 3625448968 3667329471 58021 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94239   0.14234   0.78338   0.50616   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25109 25109 SRR25822232 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz fastq fastq fastq fastq 21424338264.0 155248828.0 GSM7702835 r3 0:10 1:10 2:28 3:90 A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932 10 10 28 90 3928077020 3077672525 3451667186 3513734857 1242932 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.9433   0.14242   0.78328   0.52384   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25110 25110 SRR25822233 SRX21332628 SRS18578260 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep3 GSM7702835   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702835 GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq GSM7702835 r1 GSM7702835 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz fastq fastq fastq fastq 22542479952.0 163351304.0 GSM7702835 r4 0:10 1:10 2:28 3:90 A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485 10 10 28 90 4130174287 3235362228 3643457599 3691295761 1327485 SRX21332628 SRS18578260 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94183   0.14124   0.78301   0.50517   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25111 25111 SRR25605434 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz fastq fastq fastq fastq 20161522758.0 146097991.0 GSM7702834 r1 0:10 1:10 2:28 3:90 A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112 10 10 28 90 3649819934 2958286158 3267504300 3271384686 1824112 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94851   0.1483   0.80012   0.52549   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25112 25112 SRR25605435 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz fastq fastq fastq fastq 20708273928.0 150059956.0 GSM7702834 r2 0:10 1:10 2:28 3:90 A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351 10 10 28 90 3746088654 3037032642 3368938151 3353289242 47351 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94778   0.14581   0.80028   0.52885   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25113 25113 SRR25822230 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz fastq fastq fastq fastq 20078121078.0 145493631.0 GSM7702834 r3 0:10 1:10 2:28 3:90 A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962 10 10 28 90 3634984131 2943891505 3255149272 3259243920 1157962 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94884   0.14622   0.80099   0.52572   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25114 25114 SRR25822231 SRX21332627 SRS18578259 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep3 GSM7702834   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep3 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702834 GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq GSM7702834 r1 GSM7702834 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz fastq fastq fastq fastq 20884392978.0 151336181.0 GSM7702834 r4 0:10 1:10 2:28 3:90 A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970 10 10 28 90 3779370721 3059502508 3396295214 3383865877 1221970 SRX21332627 SRS18578259 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.94896   0.14559   0.8002   0.51418   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25115 25115 SRR25605436 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py|options: allowEarlyFileEnd 1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz fastq fastq fastq fastq 22174775364.0 160686778.0 GSM7702833 r1 0:10 1:10 2:28 3:90 A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885 10 10 28 90 4207510387 3050740898 3362227609 3839333241 1997885 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93287   0.11844   0.81087   0.55264   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25116 25116 SRR25605437 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py|options: allowEarlyFileEnd 1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz fastq fastq fastq fastq 22047847518.0 159767011.0 GSM7702833 r2 0:10 1:10 2:28 3:90 A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001 10 10 28 90 4174013532 3033959926 3357962867 3813042664 52001 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93359   0.11585   0.81087   0.55705   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25117 25117 SRR25822228 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz fastq fastq fastq fastq 22010894568.0 159499236.0 GSM7702833 r3 0:10 1:10 2:28 3:90 A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918 10 10 28 90 4176090595 3026940106 3336506731 3814128890 1264918 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93457   0.11733   0.81032   0.55203   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25118 25118 SRR25822229 SRX21332626 SRS18578258 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   gfp enriched rep2 GSM7702833   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing gfp enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702833 GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq GSM7702833 r1 GSM7702833 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz fastq fastq fastq fastq 22227220746.0 161066817.0 GSM7702833 r4 0:10 1:10 2:28 3:90 A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858 10 10 28 90 4209198596 3055507768 3382717459 3847294849 1294858 SRX21332626 SRS18578258 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.93428   0.11629   0.81014   0.56014   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25119 25119 SRR25605438 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz fastq fastq fastq fastq 25141955454.0 182188083.0 GSM7702832 r1 0:10 1:10 2:28 3:90 A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244 10 10 28 90 4942067104 3446689328 3778138998 4227670796 2361244 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90803   0.11273   0.81872   0.54345   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25120 25120 SRR25605439 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz fastq fastq fastq fastq 25433730786.0 184302397.0 GSM7702832 r2 0:10 1:10 2:28 3:90 A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122 10 10 28 90 4980326106 3488986366 3842594871 4275245265 63122 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.91035   0.11175   0.82016   0.52814   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25121 25121 SRR25822226 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz fastq fastq fastq fastq 24834656088.0 179961276.0 GSM7702832 r3 0:10 1:10 2:28 3:90 A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685 10 10 28 90 4878672093 3403443000 3732878174 4180051888 1469685 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90776   0.11325   0.81852   0.54011   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
25122 25122 SRR25822227 SRX21332625 SRS18578257 SRP454539 PRJNA1004255 Unique activities of two overlapping PAX6 retinal enhancers GSE240575 Transcriptome Analysis Enhancers play a critical role in development by precisely modulating spatial temporal and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive redundant or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.   pubmed:37643867   mcherry enriched rep2 GSM7702832   source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing mcherry enriched rep2 Cell Ranger v6.1.2 was used to perform alignment filtering barcode counting and UMI counting. A custom reference genome was created for alignment using cellranger mkref combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al. 2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size detected genes and mitochondrial reads McCarthy et al. 2017. Cells with detected genes ≥ 500 library size ≥ 800 and mitochondrial reads ≤ 10% were retained. Within the processed dataset mean reads per cell = 11239 and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al. 2019; Farnsworth et al. 2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types. Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al. 2018. SCTransform was used to perform log normalisation scaling and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted… Eye   NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.   tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf GSM7702832 GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq GSM7702832 r1 GSM7702832 1 NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution and once with FACSmax Amsbio. In a final 500 µl FACSmax the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA NextSeq 2000   SRP454539   loader:fastq load.py 1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz fastq fastq fastq fastq 25609437216.0 185575632.0 GSM7702832 r4 0:10 1:10 2:28 3:90 A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424 10 10 28 90 5015380345 3509305882 3867598814 4308011415 1510424 SRX21332625 SRS18578257 SRA1702612 Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh 1 0.90907   0.11192   0.81994   0.50902   90   B   usable mapping rate illumina nextseq_v2 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United Kingdom 2023-08-10 Hatching Embryo Eye Sensory System
34807 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;