{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Hatching\" and tissue_curation = \"Eye\"", "rows": [[19087, "ERR13834862", "ERX13237628", "ERS21098715", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC1 S20 R1 001.fastq.gz", "SAMEA116100635", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 48 HC1", "webin reads 48 HC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC1_S20_R1_001.fastq.gz", "fastq", 3768442091.0, 38065677.0, "webin reads 48 HC1", "0:99.00", "A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200", 99, null, null, null, 1055463738, 792073627, 817607736, 1103223790, 73200, "ERX13237628", "ERS21098715", "ERA30883416", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19088, "ERR13834951", "ERX13237717", "ERS21098721", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR3 S26 R1 001.fastq.gz", "58 PR3", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR3", "webin reads 58 PR3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "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, null, null, null, 1103909449, 804146524, 827344036, 1134036010, 33717, "ERX13237717", "ERS21098721", "ERA30883529", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [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", null, "retinal neurons", "58AC4 S31 R1 001.fastq.gz", "SAMEA116100646", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 58 AC4", "webin reads 58 AC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC4_S31_R1_001.fastq.gz", "fastq", 3607648651.0, 36331933.0, "webin reads 58 AC4", "0:99.30", "A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094", 99, null, null, null, 1038047870, 736262498, 759315202, 1073962987, 60094, "ERX13237776", "ERS21098726", "ERA30883721", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19090, "ERR13822794", "ERX13225546", "ERS21098708", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR2 S13 R1 001.fastq.gz", "48 PR2", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR2", "webin reads 48 PR2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR2_S13_R1_001.fastq.gz", "fastq", 3809299607.0, 38404185.0, "webin reads 48 PR2", "0:99.19", "A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777", 99, null, null, null, 1067728192, 802585802, 828435932, 1110435904, 113777, "ERX13225546", "ERS21098708", "ERA30879682", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19091, "ERR13834854", "ERX13237620", "ERS21098714", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC4 S19 R1 001.fastq.gz", "48 AC4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC4", "webin reads 48 AC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC4_S19_R1_001.fastq.gz", "fastq", 3410801894.0, 34443068.0, "webin reads 48 AC4", "0:99.03", "A:966160063;C:707754156;G:733039262;T:1003772756;N:75657", 99, null, null, null, 966160063, 707754156, 733039262, 1003772756, 75657, "ERX13237620", "ERS21098714", "ERA30883390", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19092, "ERR13828824", "ERX13231590", "ERS21098710", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR4 S15 R1 001.fastq.gz", "48 PR4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR4", "webin reads 48 PR4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR4_S15_R1_001.fastq.gz", "fastq", 4365943927.0, 44278278.0, "webin reads 48 PR4", "0:98.60", "A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503", 98, null, null, null, 1214448497, 927512154, 957491418, 1266385355, 106503, "ERX13231590", "ERS21098710", "ERA30883309", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19093, "ERR13834993", "ERX13237759", "ERS21098723", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC1 S28 R1 001.fastq.gz", "58 AC1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC1", "webin reads 58 AC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC1_S28_R1_001.fastq.gz", "fastq", 3710768269.0, 37364763.0, "webin reads 58 AC1", "0:99.31", "A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465", 99, null, null, null, 1060419097, 761984557, 786533722, 1101603428, 227465, "ERX13237759", "ERS21098723", "ERA30883659", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19094, "ERR13834875", "ERX13237641", "ERS21098717", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC3 S22 R1 001.fastq.gz", "48 HC3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 HC3", "webin reads 48 HC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC3_S22_R1_001.fastq.gz", "fastq", 3083078586.0, 31073491.0, "webin reads 48 HC3", "0:99.22", "A:856250957;C:655140994;G:677078911;T:894558582;N:49142", 99, null, null, null, 856250957, 655140994, 677078911, 894558582, 49142, "ERX13237641", "ERS21098717", "ERA30883447", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19095, "ERR13834899", "ERX13237665", "ERS21098720", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR2 S25 R1 001.fastq.gz", "58 PR2", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR2", "webin reads 58 PR2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR2_S25_R1_001.fastq.gz", "fastq", 3849571818.0, 38706841.0, "webin reads 58 PR2", "0:99.45", "A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547", 99, null, null, null, 1089593011, 803322469, 827777017, 1128836774, 42547, "ERX13237665", "ERS21098720", "ERA30883518", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19096, "ERR13834889", "ERX13237655", "ERS21098719", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR1 S24 R1 001.fastq.gz", "58 PR1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR1", "webin reads 58 PR1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR1_S24_R1_001.fastq.gz", "fastq", 3945671240.0, 39514922.0, "webin reads 58 PR1", "0:99.85", "A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802", 99, null, null, null, 1135075173, 807489123, 827964380, 1175109762, 32802, "ERX13237655", "ERS21098719", "ERA30883497", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19097, "ERR13835019", "ERX13237785", "ERS21098728", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC2 S33 R1 001.fastq.gz", "SAMEA116100648", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 58 HC2", "webin reads 58 HC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC2_S33_R1_001.fastq.gz", "fastq", 3711237069.0, 37217240.0, "webin reads 58 HC2", "0:99.72", "A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762", 99, null, null, null, 1070592288, 757099665, 780689044, 1102575310, 280762, "ERX13237785", "ERS21098728", "ERA30883748", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19100, "ERR13828836", "ERX13231602", "ERS21098712", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC2 S17 R1 001.fastq.gz", "48 AC2", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC2", "webin reads 48 AC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC2_S17_R1_001.fastq.gz", "fastq", 3205206588.0, 32424632.0, "webin reads 48 AC2", "0:98.85", "A:902438127;C:672433401;G:694813369;T:935445436;N:76255", 98, null, null, null, 902438127, 672433401, 694813369, 935445436, 76255, "ERX13231602", "ERS21098712", "ERA30883343", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19101, "ERR13835004", "ERX13237770", "ERS21098725", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC3 S30 R1 001.fastq.gz", "58 AC3", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC3", "webin reads 58 AC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC3_S30_R1_001.fastq.gz", "fastq", 3782993133.0, 38295959.0, "webin reads 58 AC3", "0:98.78", "A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531", 98, null, null, null, 1080745150, 779903026, 803258485, 1118994941, 91531, "ERX13237770", "ERS21098725", "ERA30883697", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19102, "ERR13834868", "ERX13237634", "ERS21098716", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC2 S21 R1 001.fastq.gz", "SAMEA116100636", "GIMM", "ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina", null, null, null, null, null, null, null, null, "Raw reads: 48 HC2", "webin reads 48 HC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC2_S21_R1_001.fastq.gz", "fastq", 3424347865.0, 34510204.0, "webin reads 48 HC2", "0:99.23", "A:959488173;C:721171249;G:745705870;T:997922014;N:60559", 99, null, null, null, 959488173, 721171249, 745705870, 997922014, 60559, "ERX13237634", "ERS21098716", "ERA30883434", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2024-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19104, "ERR13834880", "ERX13237646", "ERS21098718", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48HC4 S23 R1 001.fastq.gz", "48 HC4", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 HC4", "webin reads 48 HC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 HC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48HC4_S23_R1_001.fastq.gz", "fastq", 3660674315.0, 36821474.0, "webin reads 48 HC4", "0:99.42", "A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267", 99, null, null, null, 1035049987, 763030378, 788062167, 1074303516, 228267, "ERX13237646", "ERS21098718", "ERA30883470", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19105, "ERR13822867", "ERX13225633", "ERS21098709", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48PR3 S14 R1 001.fastq.gz", "48 PR3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 PR3", "webin reads 48 PR3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 PR3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48PR3_S14_R1_001.fastq.gz", "fastq", 4232170464.0, 42534853.0, "webin reads 48 PR3", "0:99.50", "A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079", 99, null, null, null, 1195251409, 889346003, 917240118, 1230272855, 60079, "ERX13225633", "ERS21098709", "ERA30879704", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19108, "ERR13828843", "ERX13234350", "ERS21098713", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC3 S18 R1 001.fastq.gz", "48 AC3", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC3", "webin reads 48 AC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC3_S18_R1_001.fastq.gz", "fastq", 3733628911.0, 37779462.0, "webin reads 48 AC3", "0:98.83", "A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473", 98, null, null, null, 1047204450, 786943605, 812327274, 1086893109, 260473, "ERX13234350", "ERS21098713", "ERA30883366", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19113, "ERR13835032", "ERX13237798", "ERS21098730", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC4 S35 R1 001.fastq.gz", "58 HC4", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC4", "webin reads 58 HC4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC4_S35_R1_001.fastq.gz", "fastq", 4418556015.0, 44331835.0, "webin reads 58 HC4", "0:99.67", "A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918", 99, null, null, null, 1255080581, 916490847, 946212615, 1300735054, 36918, "ERX13237798", "ERS21098730", "ERA30883773", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19114, "ERR13828829", "ERX13231595", "ERS21098711", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "48AC1 S16 R1 001.fastq.gz", "48 AC1", null, "organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 48 AC1", "webin reads 48 AC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 48 AC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "48AC1_S16_R1_001.fastq.gz", "fastq", 3933669121.0, 39695406.0, "webin reads 48 AC1", "0:99.10", "A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068", 99, null, null, null, 1105258159, 824538054, 854253688, 1149538152, 81068, "ERX13231595", "ERS21098711", "ERA30883326", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19117, "ERR13835025", "ERX13237791", "ERS21098729", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC3 S34 R1 001.fastq.gz", "58 HC3", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC3", "webin reads 58 HC3", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC3", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC3_S34_R1_001.fastq.gz", "fastq", 3523899212.0, 35292613.0, "webin reads 58 HC3", "0:99.85", "A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640", 99, null, null, null, 1012516999, 723225071, 745152410, 1042976092, 28640, "ERX13237791", "ERS21098729", "ERA30883757", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19118, "ERR13835014", "ERX13237780", "ERS21098727", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58HC1 S32 R1 001.fastq.gz", "58 HC1", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 HC1", "webin reads 58 HC1", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 HC1", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58HC1_S32_R1_001.fastq.gz", "fastq", 3436493821.0, 34597887.0, "webin reads 58 HC1", "0:99.33", "A:980894291;C:707196785;G:729948858;T:1018400124;N:53763", 99, null, null, null, 980894291, 707196785, 729948858, 1018400124, 53763, "ERX13237780", "ERS21098727", "ERA30883731", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19119, "ERR13834987", "ERX13237753", "ERS21098722", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58PR4 S27 R1 001.fastq.gz", "58 PR4", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 PR4", "webin reads 58 PR4", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 PR4", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58PR4_S27_R1_001.fastq.gz", "fastq", 3069040814.0, 30923422.0, "webin reads 58 PR4", "0:99.25", "A:875776938;C:633951750;G:653308475;T:905949639;N:54012", 99, null, null, null, 875776938, 633951750, 653308475, 905949639, 54012, "ERX13237753", "ERS21098722", "ERA30883641", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [19121, "ERR13834997", "ERX13237763", "ERS21098724", "ERP164534", "PRJEB80557", "RNAseq of Danio Rerio Photoreceptors  Amacrine  and Horizontal cells  collected 38  48  and 58 hpf", "e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed", "Other", "This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs  during the retinal lamination. We dissected retinae from three different developmental stages  corresponding to different stages in HCs lamination process  and separated HCs  PRs and HCs  based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed  converted to cDNA sequenced using the SMART SEQ2 protocol.", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", null, "retinal neurons", "58AC2 S29 R1 001.fastq.gz", "58 AC2", null, "organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal", null, null, null, null, null, null, null, null, "Raw reads: 58 AC2", "webin reads 58 AC2", null, null, null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq X", null, "ERP164534", "Raw reads: 58 AC2", "ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01", "58AC2_S29_R1_001.fastq.gz", "fastq", 3872162091.0, 38898173.0, "webin reads 58 AC2", "0:99.55", "A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918", 99, null, null, null, 1111663794, 793747086, 817730996, 1148980297, 39918, "ERX13237763", "ERS21098724", "ERA30883678", "Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive", "Gulbenkian Institute for Molecular Medicine", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "smartseq", null, "Belgium", "2025-01-01", "Hatching", "Embryo", "Eye", "Sensory System"], [25107, "SRR25605432", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 21603309774.0, 156545723.0, "GSM7702835 r1", "0:10 1:10 2:28 3:90", "A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216", 10, 10, 28, 90, 3960451458, 3105338977, 3480072824, 3541218595, 2033216, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94286, null, 0.14175, null, 0.78395, null, 0.51541, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25108, "SRR25605433", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 22413465270.0, 162416415.0, "GSM7702835 r2", "0:10 1:10 2:28 3:90", "A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021", 10, 10, 28, 90, 4104405257, 3220235633, 3625448968, 3667329471, 58021, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94239, null, 0.14234, null, 0.78338, null, 0.50616, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25109, "SRR25822232", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz", "fastq fastq fastq fastq", 21424338264.0, 155248828.0, "GSM7702835 r3", "0:10 1:10 2:28 3:90", "A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932", 10, 10, 28, 90, 3928077020, 3077672525, 3451667186, 3513734857, 1242932, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.9433, null, 0.14242, null, 0.78328, null, 0.52384, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25110, "SRR25822233", "SRX21332628", "SRS18578260", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep3", "GSM7702835", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702835", "GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq", "GSM7702835 r1", "GSM7702835", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 22542479952.0, 163351304.0, "GSM7702835 r4", "0:10 1:10 2:28 3:90", "A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485", 10, 10, 28, 90, 4130174287, 3235362228, 3643457599, 3691295761, 1327485, "SRX21332628", "SRS18578260", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94183, null, 0.14124, null, 0.78301, null, 0.50517, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25111, "SRR25605434", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 20161522758.0, 146097991.0, "GSM7702834 r1", "0:10 1:10 2:28 3:90", "A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112", 10, 10, 28, 90, 3649819934, 2958286158, 3267504300, 3271384686, 1824112, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94851, null, 0.1483, null, 0.80012, null, 0.52549, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25112, "SRR25605435", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 20708273928.0, 150059956.0, "GSM7702834 r2", "0:10 1:10 2:28 3:90", "A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351", 10, 10, 28, 90, 3746088654, 3037032642, 3368938151, 3353289242, 47351, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94778, null, 0.14581, null, 0.80028, null, 0.52885, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25113, "SRR25822230", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz", "fastq fastq fastq fastq", 20078121078.0, 145493631.0, "GSM7702834 r3", "0:10 1:10 2:28 3:90", "A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962", 10, 10, 28, 90, 3634984131, 2943891505, 3255149272, 3259243920, 1157962, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94884, null, 0.14622, null, 0.80099, null, 0.52572, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25114, "SRR25822231", "SRX21332627", "SRS18578259", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep3", "GSM7702834", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep3", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702834", "GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq", "GSM7702834 r1", "GSM7702834", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 20884392978.0, 151336181.0, "GSM7702834 r4", "0:10 1:10 2:28 3:90", "A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970", 10, 10, 28, 90, 3779370721, 3059502508, 3396295214, 3383865877, 1221970, "SRX21332627", "SRS18578259", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.94896, null, 0.14559, null, 0.8002, null, 0.51418, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25115, "SRR25605436", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py|options:  allowEarlyFileEnd", "1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 22174775364.0, 160686778.0, "GSM7702833 r1", "0:10 1:10 2:28 3:90", "A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885", 10, 10, 28, 90, 4207510387, 3050740898, 3362227609, 3839333241, 1997885, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93287, null, 0.11844, null, 0.81087, null, 0.55264, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25116, "SRR25605437", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py|options:  allowEarlyFileEnd", "1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 22047847518.0, 159767011.0, "GSM7702833 r2", "0:10 1:10 2:28 3:90", "A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001", 10, 10, 28, 90, 4174013532, 3033959926, 3357962867, 3813042664, 52001, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93359, null, 0.11585, null, 0.81087, null, 0.55705, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25117, "SRR25822228", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz", "fastq fastq fastq fastq", 22010894568.0, 159499236.0, "GSM7702833 r3", "0:10 1:10 2:28 3:90", "A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918", 10, 10, 28, 90, 4176090595, 3026940106, 3336506731, 3814128890, 1264918, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93457, null, 0.11733, null, 0.81032, null, 0.55203, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25118, "SRR25822229", "SRX21332626", "SRS18578258", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep2", "GSM7702833", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702833", "GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq", "GSM7702833 r1", "GSM7702833", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 22227220746.0, 161066817.0, "GSM7702833 r4", "0:10 1:10 2:28 3:90", "A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858", 10, 10, 28, 90, 4209198596, 3055507768, 3382717459, 3847294849, 1294858, "SRX21332626", "SRS18578258", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93428, null, 0.11629, null, 0.81014, null, 0.56014, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25119, "SRR25605438", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 25141955454.0, 182188083.0, "GSM7702832 r1", "0:10 1:10 2:28 3:90", "A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244", 10, 10, 28, 90, 4942067104, 3446689328, 3778138998, 4227670796, 2361244, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90803, null, 0.11273, null, 0.81872, null, 0.54345, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25120, "SRR25605439", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz", "fastq fastq fastq fastq", 25433730786.0, 184302397.0, "GSM7702832 r2", "0:10 1:10 2:28 3:90", "A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122", 10, 10, 28, 90, 4980326106, 3488986366, 3842594871, 4275245265, 63122, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.91035, null, 0.11175, null, 0.82016, null, 0.52814, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25121, "SRR25822226", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz", "fastq fastq fastq fastq", 24834656088.0, 179961276.0, "GSM7702832 r3", "0:10 1:10 2:28 3:90", "A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685", 10, 10, 28, 90, 4878672093, 3403443000, 3732878174, 4180051888, 1469685, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90776, null, 0.11325, null, 0.81852, null, 0.54011, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25122, "SRR25822227", "SRX21332625", "SRS18578257", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep2", "GSM7702832", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep2", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702832", "GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq", "GSM7702832 r1", "GSM7702832", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz", "fastq fastq fastq fastq", 25609437216.0, 185575632.0, "GSM7702832 r4", "0:10 1:10 2:28 3:90", "A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424", 10, 10, 28, 90, 5015380345, 3509305882, 3867598814, 4308011415, 1510424, "SRX21332625", "SRS18578257", "SRA1702612", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90907, null, 0.11192, null, 0.81994, null, 0.50902, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25123, "SRR25605440", "SRX21332624", "SRS18578256", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep1", "GSM7702831", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep1", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702831", "GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq", "GSM7702831 r1", "GSM7702831", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "gfp_nre_S1_L001_R2_001.fastq.gz gfp_nre_S1_L001_R1_001.fastq.gz gfp_nre_S1_L001_I2_001.fastq.gz gfp_nre_S1_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 47873499684.0, 346909418.0, "GSM7702831 r1", "0:10 1:10 2:28 3:90", "A:8912593789;C:6786299583;G:7771099171;T:7737013838;N:14841239", 10, 10, 28, 90, 8912593789, 6786299583, 7771099171, 7737013838, 14841239, "SRX21332624", "SRS18578256", "SRA1690580", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90717, null, 0.15854, null, 0.80501, null, 0.50927, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25124, "SRR25605441", "SRX21332624", "SRS18578256", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "gfp enriched rep1", "GSM7702831", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "gfp enriched rep1", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702831", "GSM7702831: gfp enriched rep1; Danio rerio; RNA Seq", "GSM7702831 r1", "GSM7702831", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "gfp_nre_S1_L002_I1_001.fastq.gz gfp_nre_S1_L002_I2_001.fastq.gz gfp_nre_S1_L002_R1_001.fastq.gz gfp_nre_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 48659347860.0, 352603970.0, "GSM7702831 r2", "0:10 1:10 2:28 3:90", "A:9056524463;C:6888387179;G:7922807308;T:7854042793;N:12595557", 10, 10, 28, 90, 9056524463, 6888387179, 7922807308, 7854042793, 12595557, "SRX21332624", "SRS18578256", "SRA1690580", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.90541, null, 0.15686, null, 0.80543, null, 0.51051, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25125, "SRR25605442", "SRX21332623", "SRS18578255", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep1", "GSM7702830", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep1", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702830", "GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq", "GSM7702830 r1", "GSM7702830", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "double_pos_S2_L001_R2_001.fastq.gz double_pos_S2_L001_R1_001.fastq.gz double_pos_S2_L001_I2_001.fastq.gz double_pos_S2_L001_I1_001.fastq.gz", "fastq fastq fastq fastq", 41371188084.0, 299791218.0, "GSM7702830 r1", "0:10 1:10 2:28 3:90", "A:7690531012;C:5787287634;G:6514950407;T:6975618202;N:12822365", 10, 10, 28, 90, 7690531012, 5787287634, 6514950407, 6975618202, 12822365, "SRX21332623", "SRS18578255", "SRA1690580", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93894, null, 0.17677, null, 0.79926, null, 0.51122, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [25126, "SRR25605443", "SRX21332623", "SRS18578255", "SRP454539", "PRJNA1004255", "Unique activities of two overlapping PAX6 retinal enhancers", "GSE240575", "Transcriptome Analysis", "Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.", null, "pubmed:37643867", null, "mcherry enriched rep1", "GSM7702830", null, "source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing", "mcherry enriched rep1", "Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes \u2265 500  library size \u2265 800  and mitochondrial reads \u2264 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using \u2018vars.to.regress\u2019. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the \u2018s.features\u2019 and \u2018g2m.features\u2019 genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file", "Eye", null, "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3\u2019 gene expression technology v3.1.", null, "tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf", "GSM7702830", "GSM7702830: mcherry enriched rep1; Danio rerio; RNA Seq", "GSM7702830 r1", "GSM7702830", "1", "NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20\u201330 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4\u00b0C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 \u00b5l FACSmax  the samples were passed through a 35 \u00b5m cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP454539", null, "loader:fastq load.py", "double_pos_S2_L002_I1_001.fastq.gz double_pos_S2_L002_I2_001.fastq.gz double_pos_S2_L002_R1_001.fastq.gz double_pos_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 42692812980.0, 309368210.0, "GSM7702830 r2", "0:10 1:10 2:28 3:90", "A:7933061913;C:5964617781;G:6744802923;T:7189579846;N:11076437", 10, 10, 28, 90, 7933061913, 5964617781, 6744802923, 7189579846, 11076437, "SRX21332623", "SRS18578255", "SRA1690580", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", "Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh", 1, 0.93887, null, 0.17578, null, 0.79825, null, 0.50169, null, 90, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-08-10", "Hatching", "Embryo", "Eye", "Sensory System"], [36381, "SRR514031", "SRX155011", "SRS346297", "SRP013815", "PRJNA168635", "Id2a knockdown in zebrafish retina", "GSE38786", "Transcriptome Analysis", "During vertebrate retinogenesis  the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways.  Moreover  there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways  which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor  Id2a  in regulating retinoblast proliferation and differentiation  with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia.  Here  we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis.  Id2a deficient retinae possess elevated levels of Notch pathway component gene expression  while retinae overexpressing id2a possess reduced expression of Notch pathway component genes.  Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity  through an RNA Seq and differential gene expression analysis of Id2a deficient retinae  we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a.  These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples", null, "pubmed:22981606", null, "Zebrafish retina with id2a morpholino treatment  replicate 2", "GSM949497", null, "source name:Zebrafish retina with id2a morpholino treatment  replicate 2|tissue:retina|genotype/variation:id2a knockdown", "Zebrafish retina with id2a morpholino treatment  replicate 2", "Filter out all reads with no call \u2018N\u2019 and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence  then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample  DESeq output for differentially expressed genes.", "Zebrafish retina with id2a morpholino treatment  replicate 2", null, "Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.", null, "tissue:retina|genotype/variation:id2a knockdown", "GSM949497", "GSM949497: Zebrafish retina with id2a morpholino treatment  replicate 2; Danio rerio; RNA Seq", "GSM949497 2", "GSM949497: Zebrafish retina with id2a morpholino treatment  replicate 2", "1", null, "GEO Accession:GSM949497", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013815", null, null, "Uribe201204_id2aKD2.untie_2.fastq.gz", "fastq", 12244707932.0, 60617366.0, "GSM949497 r1", "0:101 1:101", "A:3345422426;C:2833723441;G:2860980232;T:3204581833;N:0", 101, 101, null, null, 3345422426, 2833723441, 2860980232, 3204581833, 0, "SRX155011", "SRS346297", "SRA054377", "GEO", "Department of Biomedical Engineering, Ulsan National Institute of Science and Technology", 2, 0.8674, 0.87016, 0.09985, 0.10059, 0.75442, 0.75187, 0.47467, 0.47364, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2012-06-18", "Hatching", "Embryo", "Eye", "Sensory System"], [36382, "SRR514030", "SRX155010", "SRS346296", "SRP013815", "PRJNA168635", "Id2a knockdown in zebrafish retina", "GSE38786", "Transcriptome Analysis", "During vertebrate retinogenesis  the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways.  Moreover  there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways  which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor  Id2a  in regulating retinoblast proliferation and differentiation  with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia.  Here  we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis.  Id2a deficient retinae possess elevated levels of Notch pathway component gene expression  while retinae overexpressing id2a possess reduced expression of Notch pathway component genes.  Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity  through an RNA Seq and differential gene expression analysis of Id2a deficient retinae  we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a.  These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples", null, "pubmed:22981606", null, "Zebrafish retina with id2a morpholino treatment  replicate 1", "GSM949496", null, "source name:Zebrafish retina with id2a morpholino treatment  replicate 1|tissue:retina|genotype/variation:id2a knockdown", "Zebrafish retina with id2a morpholino treatment  replicate 1", "Filter out all reads with no call \u2018N\u2019 and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence  then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample  DESeq output for differentially expressed genes.", "Zebrafish retina with id2a morpholino treatment  replicate 1", null, "Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.", null, "tissue:retina|genotype/variation:id2a knockdown", "GSM949496", "GSM949496: Zebrafish retina with id2a morpholino treatment  replicate 1; Danio rerio; RNA Seq", "GSM949496 2", "GSM949496: Zebrafish retina with id2a morpholino treatment  replicate 1", "1", null, "GEO Accession:GSM949496", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013815", null, null, "Uribe201204_id2aKD1.untie_1.fastq.gz", "fastq", 9529605934.0, 47176267.0, "GSM949496 r1", "0:101 1:101", "A:2628394362;C:2208991321;G:2220322548;T:2471897703;N:0", 101, 101, null, null, 2628394362, 2208991321, 2220322548, 2471897703, 0, "SRX155010", "SRS346296", "SRA054377", "GEO", "Department of Biomedical Engineering, Ulsan National Institute of Science and Technology", 2, 0.83877, 0.84035, 0.0922, 0.09318, 0.76092, 0.75795, 0.48081, 0.49029, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2012-06-18", "Hatching", "Embryo", "Eye", "Sensory System"], [36383, "SRR514029", "SRX155009", "SRS346295", "SRP013815", "PRJNA168635", "Id2a knockdown in zebrafish retina", "GSE38786", "Transcriptome Analysis", "During vertebrate retinogenesis  the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways.  Moreover  there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways  which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor  Id2a  in regulating retinoblast proliferation and differentiation  with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia.  Here  we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis.  Id2a deficient retinae possess elevated levels of Notch pathway component gene expression  while retinae overexpressing id2a possess reduced expression of Notch pathway component genes.  Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity  through an RNA Seq and differential gene expression analysis of Id2a deficient retinae  we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a.  These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples", null, "pubmed:22981606", null, "Zebrafish retina with Id2aMM morpholino treatment  replicate 2", "GSM949495", null, "source name:Zebrafish retina with Id2aMM morpholino treatment  replicate 2|tissue:retina|genotype/variation:control", "Zebrafish retina with Id2aMM morpholino treatment  replicate 2", "Filter out all reads with no call \u2018N\u2019 and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence  then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample  DESeq output for differentially expressed genes.", "Zebrafish retina with Id2aMM morpholino treatment  replicate 2", null, "Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.", null, "tissue:retina|genotype/variation:control", "GSM949495", "GSM949495: Zebrafish retina with Id2aMM morpholino treatment  replicate 2; Danio rerio; RNA Seq", "GSM949495 2", "GSM949495: Zebrafish retina with Id2aMM morpholino treatment  replicate 2", "1", null, "GEO Accession:GSM949495", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013815", null, null, "Uribe201204_ctrl2.untie_2.fastq.gz", "fastq", 11102513678.0, 54962939.0, "GSM949495 r1", "0:101 1:101", "A:3114223438;C:2460129982;G:2471805247;T:3056355011;N:0", 101, 101, null, null, 3114223438, 2460129982, 2471805247, 3056355011, 0, "SRX155009", "SRS346295", "SRA054377", "GEO", "Department of Biomedical Engineering, Ulsan National Institute of Science and Technology", 2, 0.86928, 0.87394, 0.14668, 0.14966, 0.73462, 0.73428, 0.47462, 0.47615, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2012-06-18", "Hatching", "Embryo", "Eye", "Sensory System"], [36384, "SRR514028", "SRX155008", "SRS346294", "SRP013815", "PRJNA168635", "Id2a knockdown in zebrafish retina", "GSE38786", "Transcriptome Analysis", "During vertebrate retinogenesis  the precise balance between retinoblast proliferation and differentiation is spatially and temporally regulated through a number of intrinsic factors and extrinsic signaling pathways.  Moreover  there are complex gene regulatory network interactions between these intrinsic factors and extrinsic pathways  which ultimately function to determine when retinoblasts exit the cell cycle and terminally differentiate. We recently uncovered a cell non autonomous role for the intrinsic HLH factor  Id2a  in regulating retinoblast proliferation and differentiation  with Id2a deficient retinae containing an abundance of proliferative retinoblasts and an absence of terminally differentiated retinal neurons and glia.  Here  we report that Id2a function is necessary and sufficient to limit Notch pathway activity during retinogenesis.  Id2a deficient retinae possess elevated levels of Notch pathway component gene expression  while retinae overexpressing id2a possess reduced expression of Notch pathway component genes.  Attenuation of Notch signaling activity by DAPT or by morpholino knockdown of Notch1a is sufficient to rescue both the proliferative and differentiation defects in Id2a deficient retinae. In addition to regulating Notch pathway activity  through an RNA Seq and differential gene expression analysis of Id2a deficient retinae  we identify a number of additional intrinsic and extrinsic regulatory pathway components whose expression is regulated by Id2a.  These data highlight the integral role played by Id2a in the gene regulatory network governing the transition from retinoblast proliferation to terminal differentiation during vertebrate retinogenesis. Overall design: Two biological replicates for both Id2aMM and Id2aMO samples", null, "pubmed:22981606", null, "Zebrafish retina with Id2aMM morpholino treatment  replicate 1", "GSM949494", null, "source name:Zebrafish retina with Id2aMM morpholino treatment  replicate 1|tissue:retina|genotype/variation:control", "Zebrafish retina with Id2aMM morpholino treatment  replicate 1", "Filter out all reads with no call \u2018N\u2019 and low complexity reads without xxx 4 bases. Take reads that both paired end reads are passed the above condition. Map to EnsEMBL cDNA sequence  then calculate RPK100M read counts per kb per 100 million of reads Summarize mapped reads per each cDNA. Determine differentially expressed genes with DESeq Genome build: EnsEMBL version 66 cDNA sequences Supplementary files format and content: tab delimited text files include RPKM values for each Sample  DESeq output for differentially expressed genes.", "Zebrafish retina with Id2aMM morpholino treatment  replicate 1", null, "Total RNA was isolated from dissected retinae at 48 hpf using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 microgram of total retinal RNA per condition to generate cDNA libraries by poly A selection.", null, "tissue:retina|genotype/variation:control", "GSM949494", "GSM949494: Zebrafish retina with Id2aMM morpholino treatment  replicate 1; Danio rerio; RNA Seq", "GSM949494 2", "GSM949494: Zebrafish retina with Id2aMM morpholino treatment  replicate 1", "1", null, "GEO Accession:GSM949494", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013815", null, null, "Uribe201204_ctrl1.untie_1.fastq.gz", "fastq", 9965568192.0, 49334496.0, "GSM949494 r1", "0:101 1:101", "A:2748582966;C:2261528563;G:2269950332;T:2685506331;N:0", 101, 101, null, null, 2748582966, 2261528563, 2269950332, 2685506331, 0, "SRX155008", "SRS346294", "SRA054377", "GEO", "Department of Biomedical Engineering, Ulsan National Institute of Science and Technology", 2, 0.86051, 0.86328, 0.11721, 0.11892, 0.74184, 0.74075, 0.47603, 0.47166, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2012-06-18", "Hatching", "Embryo", "Eye", "Sensory System"], [49320, "SRR7886615", "SRX4724267", "SRS3809041", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60MGS3", "GSM3397449", null, "source name:60hpf GFAP:GFP Positive|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "60MGS3", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397449", "GSM3397449: 60MGS3; Danio rerio; RNA Seq", "GSM3397449", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397449", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60MGS3.bam", "bam", 2508986250.0, 20071890.0, "GSM3397449 r1", "0:125", "A:633150258;C:658892300;G:571953995;T:644986169;N:3528", 125, null, null, null, 633150258, 658892300, 571953995, 644986169, 3528, "SRX4724267", "SRS3809041", "SRA780762", "GEO", "University of Cambridge", 1, 0.0112, null, 0.00292, null, 0.98711, null, 0.60601, null, 125, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49321, "SRR7886614", "SRX4724266", "SRS3809040", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60MGS2", "GSM3397448", null, "source name:60hpf GFAP:GFP Positive|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "60MGS2", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397448", "GSM3397448: 60MGS2; Danio rerio; RNA Seq", "GSM3397448", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397448", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60MGS2.bam", "bam", 2600602375.0, 20804819.0, "GSM3397448 r1", "0:125", "A:676529819;C:637723743;G:635912971;T:650421922;N:13920", 125, null, null, null, 676529819, 637723743, 635912971, 650421922, 13920, "SRX4724266", "SRS3809040", "SRA780762", "GEO", "University of Cambridge", 1, 0.01123, null, 0.00282, null, 0.98713, null, 0.59463, null, 125, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49322, "SRR7886613", "SRX4724265", "SRS3809039", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60MGS1", "GSM3397447", null, "source name:60hpf GFAP:GFP Positive|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "60MGS1", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397447", "GSM3397447: 60MGS1; Danio rerio; RNA Seq", "GSM3397447", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397447", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60MGS1.bam", "bam", 2600602375.0, 20804819.0, "GSM3397447 r1", "0:125", "A:656042019;C:682911096;G:592791803;T:668797312;N:60145", 125, null, null, null, 656042019, 682911096, 592791803, 668797312, 60145, "SRX4724265", "SRS3809039", "SRA780762", "GEO", "University of Cambridge", 1, 0.01127, null, 0.00304, null, 0.98754, null, 0.6105, null, 125, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49323, "SRR7886612", "SRX4724264", "SRS3809038", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60CS3", "GSM3397446", null, "source name:60hpf GFAP:GFP Negative|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "60CS3", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397446", "GSM3397446: 60CS3; Danio rerio; RNA Seq", "GSM3397446", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397446", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60CS3.bam", "bam", 3217257000.0, 25738056.0, "GSM3397446 r1", "0:125", "A:856598472;C:777828660;G:710658273;T:872152518;N:19077", 125, null, null, null, 856598472, 777828660, 710658273, 872152518, 19077, "SRX4724264", "SRS3809038", "SRA780762", "GEO", "University of Cambridge", 1, 0.4529, null, 0.05353, null, 0.79701, null, 0.55977, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49324, "SRR7886611", "SRX4724263", "SRS3809037", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60CS2", "GSM3397445", null, "source name:60hpf GFAP:GFP Negative|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "60CS2", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397445", "GSM3397445: 60CS2; Danio rerio; RNA Seq", "GSM3397445", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397445", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60CS2.bam", "bam", 3308467000.0, 26467736.0, "GSM3397445 r1", "0:125", "A:898472326;C:766795565;G:762042071;T:881139599;N:17439", 125, null, null, null, 898472326, 766795565, 762042071, 881139599, 17439, "SRX4724263", "SRS3809037", "SRA780762", "GEO", "University of Cambridge", 1, 0.44529, null, 0.05447, null, 0.80273, null, 0.53894, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49325, "SRR7886610", "SRX4724262", "SRS3809036", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "60CS1", "GSM3397444", null, "source name:60hpf GFAP:GFP Negative|age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "60CS1", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "60hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:60hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397444", "GSM3397444: 60CS1; Danio rerio; RNA Seq", "GSM3397444", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397444", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "60CS1.bam", "bam", 3308467000.0, 26467736.0, "GSM3397444 r1", "0:125", "A:881969824;C:799783674;G:727574215;T:899065817;N:73470", 125, null, null, null, 881969824, 799783674, 727574215, 899065817, 73470, "SRX4724262", "SRS3809036", "SRA780762", "GEO", "University of Cambridge", 1, 0.44178, null, 0.05281, null, 0.79849, null, 0.54471, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49326, "SRR7886609", "SRX4724261", "SRS3809035", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48MGS3", "GSM3397443", null, "source name:48hpf GFAP:GFP Positive|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "48MGS3", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397443", "GSM3397443: 48MGS3; Danio rerio; RNA Seq", "GSM3397443", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397443", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48MGS3.bam", "bam", 3751483125.0, 30011865.0, "GSM3397443 r1", "0:125", "A:1063899440;C:813181012;G:740633593;T:1133592737;N:176343", 125, null, null, null, 1063899440, 813181012, 740633593, 1133592737, 176343, "SRX4724261", "SRS3809035", "SRA780762", "GEO", "University of Cambridge", 1, 0.87448, null, 0.46322, null, 0.85437, null, 0.46617, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49327, "SRR7886608", "SRX4724260", "SRS3809034", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48MGS2", "GSM3397442", null, "source name:48hpf GFAP:GFP Positive|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "48MGS2", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397442", "GSM3397442: 48MGS2; Danio rerio; RNA Seq", "GSM3397442", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397442", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48MGS2.bam", "bam", 3253082750.0, 26024662.0, "GSM3397442 r1", "0:125", "A:860727696;C:787565434;G:719641544;T:885087745;N:60331", 125, null, null, null, 860727696, 787565434, 719641544, 885087745, 60331, "SRX4724260", "SRS3809034", "SRA780762", "GEO", "University of Cambridge", 1, 0.70949, null, 0.06764, null, 0.79251, null, 0.56599, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49328, "SRR7886607", "SRX4724259", "SRS3809033", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48MGS1", "GSM3397441", null, "source name:48hpf GFAP:GFP Positive|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "48MGS1", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Positive", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Positive", "GSM3397441", "GSM3397441: 48MGS1; Danio rerio; RNA Seq", "GSM3397441", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48MGS1.bam", "bam", 3155766875.0, 25246135.0, "GSM3397441 r1", "0:125", "A:835678187;C:762799231;G:696339226;T:860875540;N:74691", 125, null, null, null, 835678187, 762799231, 696339226, 860875540, 74691, "SRX4724259", "SRS3809033", "SRA780762", "GEO", "University of Cambridge", 1, 0.70755, null, 0.06855, null, 0.79569, null, 0.53396, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49329, "SRR7886606", "SRX4724258", "SRS3809032", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48CS3", "GSM3397440", null, "source name:48hpf GFAP:GFP Negative|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "48CS3", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397440", "GSM3397440: 48CS3; Danio rerio; RNA Seq", "GSM3397440", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48CS3.bam", "bam", 662621625.0, 5300973.0, "GSM3397440 r1", "0:125", "A:179417199;C:153458866;G:152649509;T:177095017;N:1034", 125, null, null, null, 179417199, 153458866, 152649509, 177095017, 1034, "SRX4724258", "SRS3809032", "SRA780762", "GEO", "University of Cambridge", 1, 0.70566, null, 0.06917, null, 0.79488, null, 0.58099, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49330, "SRR7886605", "SRX4724257", "SRS3809031", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48CS2", "GSM3397439", null, "source name:48hpf GFAP:GFP Negative|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "48CS2", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397439", "GSM3397439: 48CS2; Danio rerio; RNA Seq", "GSM3397439", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48CS2.bam", "bam", 959630000.0, 7677040.0, "GSM3397439 r1", "0:125", "A:250545467;C:236640013;G:213639661;T:258800686;N:4173", 125, null, null, null, 250545467, 236640013, 213639661, 258800686, 4173, "SRX4724257", "SRS3809031", "SRA780762", "GEO", "University of Cambridge", 1, 0.55605, null, 0.07819, null, 0.80186, null, 0.59736, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [49331, "SRR7886604", "SRX4724256", "SRS3809030", "SRP162288", "PRJNA492363", "Genetic control of cellular morphogenesis in M\u00fcller glia", "GSE120275", "Transcriptome Analysis", "How the various cell types of the body achieve their specific shapes is fundamentally unknown.  Here  we explore this issue by identifying genes involved in the elaboration of the complex  yet conserved  cellular morphology of M\u00fcller glial MG cells in the retina.  Using genomic  based strategies in zebrafish  we found more than 40 candidate genes involved in specific aspects of MG morphogenesis.  The successive steps of cell morphogenesis correlate with the timing of the expression of cohorts of inter related genes that have roles in generating the particular anatomical features of these cells  suggesting that a sequence of genetic regulomes govern stepwise cellular morphogenesis in this system. Overall design: 12 samples with three replicates each are provided.  GFAP:GFP positive and negative cells were FAC sorted from wild type animals from each developmental stage", null, "pubmed:30924555", null, "48CS1", "GSM3397438", null, "source name:48hpf GFAP:GFP Negative|age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "48CS1", "Trimmomatic read trimming Hisat2 genome aligment Samtools Sam to Bam sorting Bioconuducter Feature counts  Rsubread  limma DESeq2  DEFormats  org.Dr.eg.db  EdgeR Genome build: GRCz10 Supplementary files format and content: TMM fold change analysis", "48hpf GFAP:GFP Negative", null, "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer\u2019s protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", null, "age:48hpf|genotype:Control GFAP:GFP|tissue:Dissociated retinal tissue|gfap:Negative", "GSM3397438", "GSM3397438: 48CS1; Danio rerio; RNA Seq", "GSM3397438", null, "1", "Single cell suspensions were sorted on a Beckman Coulter MoFlo to capture Muller glia GFP and control retinal tissue non GFP. Cells were sorted into lysis buffer  and RNA was immediately extracted using the RNeasy mini kit Qiagen. RNA concentration and qualities were assessed on an Agilent Bioanalyzer and RNA amplification and cDNA synthesis was performed with the Ovation RNA Amplification System V2 NuGEN using manufacturer's protocol. Nextera library preparations were performed using the Nextera DNA library kit according to the manufacturer's directions", "GEO Accession:GSM3397438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162288", null, "dangling references:treat as unmapped", "48CS1.bam", "bam", 959630000.0, 7677040.0, "GSM3397438 r1", "0:125", "A:248562218;C:241973573;G:206301549;T:262772093;N:20567", 125, null, null, null, 248562218, 241973573, 206301549, 262772093, 20567, "SRX4724256", "SRS3809030", "SRA780762", "GEO", "University of Cambridge", 1, 0.55246, null, 0.07651, null, 0.79659, null, 0.6137, null, 125, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "nextera", "bulk", "unknown", "unknown", null, "United Kingdom", "2018-09-20", "Hatching", "Embryo", "Eye", "Sensory System"], [50656, "SRR10769144", "SRX7443062", "SRS5887360", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "48 hpf retina rep", "GSM4233148", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "48 hpf retina rep", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data  we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We subtract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples  we subtract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv  genes.tsv  matrix.mtx", "Retina", null, "We dissected 24   36   48   72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution  the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "GSM4233148", "GSM4233148: 48 hpf retina rep; Danio rerio; RNA Seq", "GSM4233148", null, "1", "We dissected 24   36   48   72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution  the GFP positive cells which could label the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM4233148", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, "intentional duplicate", "48hpf_rep_possorted_genome_bam.bam", "10X Genomics bam file", 31477860150.0, 209852401.0, "GSM4233148 r1", "0:150", "A:9531250692;C:6384514147;G:7053602060;T:8508157890;N:335361", 150, null, null, null, 9531250692, 6384514147, 7053602060, 8508157890, 335361, "SRX7443062", "SRS5887360", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.91107, null, 0.07208, null, 0.83644, null, 0.47681, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2019-12-26", "Hatching", "Embryo", "Eye", "Sensory System"], [50661, "SRR11812054", "SRX5025779", "SRS4057279", "SRP169565", "PRJNA506002", "Unifying Developmental Programs for Embryonic and Post Embryonic Neurogenesis in the Zebrafish Retina", "GSE122680", "Transcriptome Analysis", "It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post embryonic neurogenic programs in the vertebrate retina. Overall design: Retinal samples from 4 developmental stages and 1 post embryonic stage", null, "pubmed:32467236", null, "48 hpf retina", "GSM3478015", null, "source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "48 hpf retina", "Single cell FASTQ sequencing reads Novogene aligned to the zebrafish genome Zv10 were processed and converted to digital gene expression matrices using the Cell Ranger Single Cell Software Suite v2.1.0 provided in 10x genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. To further analyze the data  we used an analysis pipeline provided by the Seurat R package http://satijalab.org/seurat/. We substract progenitor cell clusters of 36hpf and 48hpf samples according to the proliferative gene expression. For post embryonic samples  we substract the ciliary marginal zone CMZ cell clusters based on marker genes' expression. Genome build: Zv10 Supplementary files format and content: barcodes.tsv  genes.tsv  matrix.mtx", "Retina", null, "We dissected 24   36   48   72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution  the GFP positive cells which could label  the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer\u2019s protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer\u2019s protocol.", null, "strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:48 hpf", "GSM3478015", "GSM3478015: 48 hpf retina; Danio rerio; RNA Seq", "GSM3478015", null, "1", "We dissected 24   36   48   72 hpf retinas of wild type zebrafishes and isolated via papin solution. 14 dpf retinas were dissected from PCNA GFP transgenic fishes. And post isolation by papin solution  the GFP positive cells which could label  the ciliary marginal zone CMZ cells were sorted via FACS. These isolated cells filtered by 40\u03bcm cell strainer BD Falcon were loaded onto the Chromium Single Cell Chip10x Genomics according to the manufacturer's protocol. Single cell RNA seq libraries were generated using the GemCode Single Cell Instrument and Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x Genomics following the manufacturer's protocol.", "GEO Accession:GSM3478015", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP169565", null, "intentional duplicate", "48hpf_possorted_genome_bam.bam", "10X Genomics bam file", 27828827400.0, 185525516.0, "GSM3478015 r11", "0:150", "A:8568529313;C:5431445717;G:5968188905;T:7860573445;N:90020", 150, null, null, null, 8568529313, 5431445717, 5968188905, 7860573445, 90020, "SRX5025779", "SRS4057279", "SRA812747", "GEO", "Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS", 1, 0.91308, null, 0.11004, null, 0.82213, null, 0.48772, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-11-19", "Hatching", "Embryo", "Eye", "Sensory System"], [61581, "SRR12874662", "SRX9340686", "SRS7562493", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 56 hpf Rep5 [5 56 R]", "GSM4848085", null, "source name:dorsal retina 56 hpf|hpf:56|tissue:dorsal retina", "DR 56 hpf Rep5 [5 56 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:dorsal retina", "GSM4848085", "GSM4848085: DR 56 hpf Rep5 [5 56 R]; Danio rerio; RNA Seq", "GSM4848085", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848085", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "5-56-R_R1.fastq.gz 5-56-R_R2.fastq.gz", "fastq fastq", 3021678200.0, 15108391.0, "GSM4848085 r1", "0:100 1:100", "A:842653749;C:670303060;G:690387728;T:815456479;N:2877184", 100, 100, null, null, 842653749, 670303060, 690387728, 815456479, 2877184, "SRX9340686", "SRS7562493", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94619, 0.94623, 0.15083, 0.1507, 0.74639, 0.74834, 0.48701, 0.49558, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61582, "SRR12874661", "SRX9340685", "SRS7562495", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep5 [5 56 0]", "GSM4848084", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep5 [5 56 0]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848084", "GSM4848084: OF 56 hpf Rep5 [5 56 0]; Danio rerio; RNA Seq", "GSM4848084", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848084", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "5-56-O_R1.fastq.gz 5-56-O_R2.fastq.gz", "fastq fastq", 2975878600.0, 14879393.0, "GSM4848084 r1", "0:100 1:100", "A:837964142;C:651309804;G:674797335;T:808675013;N:3132306", 100, 100, null, null, 837964142, 651309804, 674797335, 808675013, 3132306, "SRX9340685", "SRS7562495", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94334, 0.94301, 0.17167, 0.17156, 0.7376, 0.73764, 0.48724, 0.48286, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61583, "SRR12874660", "SRX9340684", "SRS7562494", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 48 hpf Rep5 [5 48 R]", "GSM4848083", null, "source name:dorsal retina 48 hpf|hpf:48|tissue:dorsal retina", "DR 48 hpf Rep5 [5 48 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:dorsal retina", "GSM4848083", "GSM4848083: DR 48 hpf Rep5 [5 48 R]; Danio rerio; RNA Seq", "GSM4848083", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848083", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "5-48-R_R1.fastq.gz 5-48-R_R2.fastq.gz", "fastq fastq", 2239921200.0, 11199606.0, "GSM4848083 r1", "0:100 1:100", "A:625661378;C:494955850;G:511675170;T:605386182;N:2242620", 100, 100, null, null, 625661378, 494955850, 511675170, 605386182, 2242620, "SRX9340684", "SRS7562494", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94552, 0.9457, 0.15214, 0.1519, 0.7431, 0.74381, 0.49047, 0.48932, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61584, "SRR12874659", "SRX9340683", "SRS7562492", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 48 hpf Rep5 [5 48 O]", "GSM4848082", null, "source name:optic fissure retina 48 hpf|hpf:48|tissue:optic fissure retina", "OF 48 hpf Rep5 [5 48 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:optic fissure retina", "GSM4848082", "GSM4848082: OF 48 hpf Rep5 [5 48 O]; Danio rerio; RNA Seq", "GSM4848082", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848082", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "5-48-O_R1.fastq.gz 5-48-O_R2.fastq.gz", "fastq fastq", 2833605600.0, 14168028.0, "GSM4848082 r1", "0:100 1:100", "A:788130966;C:630887942;G:649916615;T:761868221;N:2801856", 100, 100, null, null, 788130966, 630887942, 649916615, 761868221, 2801856, "SRX9340683", "SRS7562492", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94695, 0.94729, 0.14775, 0.14824, 0.73953, 0.74164, 0.49175, 0.4918, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61587, "SRR12874656", "SRX9340680", "SRS7562490", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 56 hpf Rep4 [4 56 R]", "GSM4848079", null, "source name:dorsal retina 56 hpf|hpf:56|tissue:dorsal retina", "DR 56 hpf Rep4 [4 56 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:dorsal retina", "GSM4848079", "GSM4848079: DR 56 hpf Rep4 [4 56 R]; Danio rerio; RNA Seq", "GSM4848079", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848079", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "4-56-R_R1.fastq.gz 4-56-R_R2.fastq.gz", "fastq fastq", 2575355000.0, 12876775.0, "GSM4848079 r1", "0:100 1:100", "A:719372734;C:569208001;G:591353722;T:692825451;N:2595092", 100, 100, null, null, 719372734, 569208001, 591353722, 692825451, 2595092, "SRX9340680", "SRS7562490", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94196, 0.94214, 0.14248, 0.14239, 0.74519, 0.74556, 0.48766, 0.48749, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61588, "SRR12874655", "SRX9340679", "SRS7562488", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep4 [4 56 O]", "GSM4848078", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep4 [4 56 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848078", "GSM4848078: OF 56 hpf Rep4 [4 56 O]; Danio rerio; RNA Seq", "GSM4848078", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848078", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "4-56-O_R1.fastq.gz 4-56-O_R2.fastq.gz", "fastq fastq", 2962950600.0, 14814753.0, "GSM4848078 r1", "0:100 1:100", "A:839363055;C:643262435;G:667200849;T:810187958;N:2936303", 100, 100, null, null, 839363055, 643262435, 667200849, 810187958, 2936303, "SRX9340679", "SRS7562488", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93382, 0.93302, 0.17575, 0.17531, 0.74085, 0.74223, 0.49824, 0.504, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61589, "SRR12874654", "SRX9340678", "SRS7562487", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 48 hpf Rep4 [4 48 R]", "GSM4848077", null, "source name:dorsal retina 48 hpf|hpf:48|tissue:dorsal retina", "DR 48 hpf Rep4 [4 48 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:dorsal retina", "GSM4848077", "GSM4848077: DR 48 hpf Rep4 [4 48 R]; Danio rerio; RNA Seq", "GSM4848077", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848077", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "4-48-R_R1.fastq.gz 4-48-R_R2.fastq.gz", "fastq fastq", 2844671200.0, 14223356.0, "GSM4848077 r1", "0:100 1:100", "A:794974141;C:628655166;G:651606298;T:766506062;N:2929533", 100, 100, null, null, 794974141, 628655166, 651606298, 766506062, 2929533, "SRX9340678", "SRS7562487", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94228, 0.94286, 0.14952, 0.1508, 0.7558, 0.75621, 0.49161, 0.49112, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61590, "SRR12874653", "SRX9340677", "SRS7562486", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 48 hpf Rep4 [4 48 O]", "GSM4848076", null, "source name:optic fissure retina 48 hpf|hpf:48|tissue:optic fissure retina", "OF 48 hpf Rep4 [4 48 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:optic fissure retina", "GSM4848076", "GSM4848076: OF 48 hpf Rep4 [4 48 O]; Danio rerio; RNA Seq", "GSM4848076", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848076", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "4-48-O_R1.fastq.gz 4-48-O_R2.fastq.gz", "fastq fastq", 2972787000.0, 14863935.0, "GSM4848076 r1", "0:100 1:100", "A:831928443;C:656429034;G:674981859;T:806440139;N:3007525", 100, 100, null, null, 831928443, 656429034, 674981859, 806440139, 3007525, "SRX9340677", "SRS7562486", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94047, 0.93996, 0.16117, 0.1608, 0.743, 0.74533, 0.48986, 0.49728, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61593, "SRR12874650", "SRX9340674", "SRS7562482", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 56 hpf Rep3 [3 56 R]", "GSM4848073", null, "source name:dorsal retina 56 hpf|hpf:56|tissue:dorsal retina", "DR 56 hpf Rep3 [3 56 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:dorsal retina", "GSM4848073", "GSM4848073: DR 56 hpf Rep3 [3 56 R]; Danio rerio; RNA Seq", "GSM4848073", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848073", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "3-56-R_R1.fastq.gz 3-56-R_R2.fastq.gz", "fastq fastq", 2836655800.0, 14183279.0, "GSM4848073 r1", "0:100 1:100", "A:796999987;C:622654837;G:648405815;T:765641148;N:2954013", 100, 100, null, null, 796999987, 622654837, 648405815, 765641148, 2954013, "SRX9340674", "SRS7562482", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94067, 0.94077, 0.15638, 0.15562, 0.74403, 0.74497, 0.49593, 0.49546, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61594, "SRR12874649", "SRX9340673", "SRS7562484", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep3 [3 56 O]", "GSM4848072", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep3 [3 56 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848072", "GSM4848072: OF 56 hpf Rep3 [3 56 O]; Danio rerio; RNA Seq", "GSM4848072", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848072", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "3-56-O_R1.fastq.gz 3-56-O_R2.fastq.gz", "fastq fastq", 2962222200.0, 14811111.0, "GSM4848072 r1", "0:100 1:100", "A:839522002;C:642451913;G:665094462;T:812146216;N:3007607", 100, 100, null, null, 839522002, 642451913, 665094462, 812146216, 3007607, "SRX9340673", "SRS7562484", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93685, 0.93543, 0.17034, 0.17106, 0.73914, 0.74087, 0.49394, 0.4949, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61595, "SRR12874648", "SRX9340672", "SRS7562481", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 48 hpf Rep3 [3 48 R]", "GSM4848071", null, "source name:dorsal retina 48 hpf|hpf:48|tissue:dorsal retina", "DR 48 hpf Rep3 [3 48 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:dorsal retina", "GSM4848071", "GSM4848071: DR 48 hpf Rep3 [3 48 R]; Danio rerio; RNA Seq", "GSM4848071", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848071", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "3-48-R_R1.fastq.gz 3-48-R_R2.fastq.gz", "fastq fastq", 3015560600.0, 15077803.0, "GSM4848071 r1", "0:100 1:100", "A:857335603;C:650996829;G:676858466;T:827306581;N:3063121", 100, 100, null, null, 857335603, 650996829, 676858466, 827306581, 3063121, "SRX9340672", "SRS7562481", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.92909, 0.92812, 0.17933, 0.17852, 0.75708, 0.75903, 0.45933, 0.50484, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61596, "SRR12874647", "SRX9340671", "SRS7562480", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 48 hpf Rep3 [3 48 O]", "GSM4848070", null, "source name:optic fissure retina 48 hpf|hpf:48|tissue:optic fissure retina", "OF 48 hpf Rep3 [3 48 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:optic fissure retina", "GSM4848070", "GSM4848070: OF 48 hpf Rep3 [3 48 O]; Danio rerio; RNA Seq", "GSM4848070", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848070", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "3-48-O_R1.fastq.gz 3-48-O_R2.fastq.gz", "fastq fastq", 3617936400.0, 18089682.0, "GSM4848070 r1", "0:100 1:100", "A:1017979863;C:791826181;G:821834684;T:982508058;N:3787614", 100, 100, null, null, 1017979863, 791826181, 821834684, 982508058, 3787614, "SRX9340671", "SRS7562480", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93482, 0.93556, 0.17727, 0.1779, 0.73217, 0.73267, 0.49331, 0.49384, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61599, "SRR12874644", "SRX9340668", "SRS7562477", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 56 hpf Rep2 [2 56 R]", "GSM4848067", null, "source name:dorsal retina 56 hpf|hpf:56|tissue:dorsal retina", "DR 56 hpf Rep2 [2 56 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:dorsal retina", "GSM4848067", "GSM4848067: DR 56 hpf Rep2 [2 56 R]; Danio rerio; RNA Seq", "GSM4848067", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848067", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "2-56-R_R1.fastq.gz 2-56-R_R2.fastq.gz", "fastq fastq", 2736567000.0, 13682835.0, "GSM4848067 r1", "0:100 1:100", "A:774624618;C:594658601;G:615415962;T:749131027;N:2736792", 100, 100, null, null, 774624618, 594658601, 615415962, 749131027, 2736792, "SRX9340668", "SRS7562477", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93368, 0.93451, 0.17403, 0.17569, 0.74201, 0.74479, 0.5181, 0.50551, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61600, "SRR12874643", "SRX9340667", "SRS7562476", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep2 [2 56 O]", "GSM4848066", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep2 [2 56 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848066", "GSM4848066: OF 56 hpf Rep2 [2 56 O]; Danio rerio; RNA Seq", "GSM4848066", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848066", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "2-56-O_R1.fastq.gz 2-56-O_R2.fastq.gz", "fastq fastq", 2676334400.0, 13381672.0, "GSM4848066 r1", "0:100 1:100", "A:755448065;C:583050210;G:604376373;T:730670069;N:2789683", 100, 100, null, null, 755448065, 583050210, 604376373, 730670069, 2789683, "SRX9340667", "SRS7562476", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93546, 0.93514, 0.19101, 0.19201, 0.72088, 0.7217, 0.4938, 0.48928, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61601, "SRR12874642", "SRX9340666", "SRS7562475", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 48 hpf Rep2 [2 48 R]", "GSM4848065", null, "source name:dorsal retina 48 hpf|hpf:48|tissue:dorsal retina", "DR 48 hpf Rep2 [2 48 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:dorsal retina", "GSM4848065", "GSM4848065: DR 48 hpf Rep2 [2 48 R]; Danio rerio; RNA Seq", "GSM4848065", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848065", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "2-48-R_R1.fastq.gz 2-48-R_R2.fastq.gz", "fastq fastq", 3092140600.0, 15460703.0, "GSM4848065 r1", "0:100 1:100", "A:865594525;C:682549898;G:702370234;T:838685013;N:2940930", 100, 100, null, null, 865594525, 682549898, 702370234, 838685013, 2940930, "SRX9340666", "SRS7562475", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.94438, 0.94383, 0.14587, 0.1461, 0.74211, 0.74464, 0.50115, 0.50098, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61602, "SRR12874641", "SRX9340665", "SRS7562474", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 48 hpf Rep2 [2 48 O]", "GSM4848064", null, "source name:optic fissure retina 48 hpf|hpf:48|tissue:optic fissure retina", "OF 48 hpf Rep2 [2 48 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:optic fissure retina", "GSM4848064", "GSM4848064: OF 48 hpf Rep2 [2 48 O]; Danio rerio; RNA Seq", "GSM4848064", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848064", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "2-48-O_R1.fastq.gz 2-48-O_R2.fastq.gz", "fastq fastq", 2606582200.0, 13032911.0, "GSM4848064 r1", "0:100 1:100", "A:739206672;C:564781083;G:586126893;T:713698007;N:2769545", 100, 100, null, null, 739206672, 564781083, 586126893, 713698007, 2769545, "SRX9340665", "SRS7562474", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93607, 0.93608, 0.18238, 0.18202, 0.72719, 0.72827, 0.49891, 0.49686, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61605, "SRR12874638", "SRX9340662", "SRS7562471", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 56 hpf Rep1 [1 56 R]", "GSM4848061", null, "source name:dorsal retina 56 hpf|hpf:56|tissue:dorsal retina", "DR 56 hpf Rep1 [1 56 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:dorsal retina", "GSM4848061", "GSM4848061: DR 56 hpf Rep1 [1 56 R]; Danio rerio; RNA Seq", "GSM4848061", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "1-56-R_R1.fastq.gz 1-56-R_R2.fastq.gz", "fastq fastq", 2657160200.0, 13285801.0, "GSM4848061 r1", "0:100 1:100", "A:783255245;C:545277836;G:561089398;T:764970589;N:2567132", 100, 100, null, null, 783255245, 545277836, 561089398, 764970589, 2567132, "SRX9340662", "SRS7562471", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.89392, 0.89321, 0.38815, 0.38896, 0.70516, 0.70565, 0.5057, 0.49386, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61606, "SRR12874637", "SRX9340661", "SRS7562470", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 56 hpf Rep1 [1 56 O]", "GSM4848060", null, "source name:optic fissure retina 56 hpf|hpf:56|tissue:optic fissure retina", "OF 56 hpf Rep1 [1 56 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 56 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:56|tissue:optic fissure retina", "GSM4848060", "GSM4848060: OF 56 hpf Rep1 [1 56 O]; Danio rerio; RNA Seq", "GSM4848060", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "1-56-O_R1.fastq.gz 1-56-O_R2.fastq.gz", "fastq fastq", 2610698400.0, 13053492.0, "GSM4848060 r1", "0:100 1:100", "A:747164488;C:558793373;G:578023357;T:723973829;N:2743353", 100, 100, null, null, 747164488, 558793373, 578023357, 723973829, 2743353, "SRX9340661", "SRS7562470", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.92606, 0.92637, 0.20702, 0.20634, 0.72056, 0.72121, 0.50668, 0.50793, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61607, "SRR12874636", "SRX9340660", "SRS7562469", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "DR 48 hpf Rep1 [1 48 R]", "GSM4848059", null, "source name:dorsal retina 48 hpf|hpf:48|tissue:dorsal retina", "DR 48 hpf Rep1 [1 48 R]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "dorsal retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:dorsal retina", "GSM4848059", "GSM4848059: DR 48 hpf Rep1 [1 48 R]; Danio rerio; RNA Seq", "GSM4848059", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848059", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "1-48-R_R1.fastq.gz 1-48-R_R2.fastq.gz", "fastq fastq", 2342612000.0, 11713060.0, "GSM4848059 r1", "0:100 1:100", "A:660019342;C:511509124;G:533952026;T:634790133;N:2341375", 100, 100, null, null, 660019342, 511509124, 533952026, 634790133, 2341375, "SRX9340660", "SRS7562469", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93651, 0.93755, 0.17081, 0.17042, 0.74194, 0.74322, 0.50319, 0.50384, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [61608, "SRR12874635", "SRX9340659", "SRS7562467", "SRP288083", "PRJNA670550", "Transcriptome profiling of zebrafish optic fissure fusion", "GSE159822", "Transcriptome Analysis", "Incomplete fusion of the optic fissure leads to ocular coloboma  a congenital eye defect that affects up to 7.5 per 10 000 births and accounts for up to 10 percent of childhood blindness. The molecular and cellular mechanisms that facilitate optic fissure fusion remain elusive. We have profiled global gene expression during optic fissure morphogenesis by transcriptome analysis of tissue dissected from the margins of the zebrafish optic fissure and the opposing dorsal retina before 32 hpf  hpf  during 48 hpf and post 56 hpf optic fissure fusion. Differential expression analysis between optic fissure and dorsal retinal tissue resulted in the detection of several known and novel developmental genes. The expression of selected genes was validated by qRT PCR analysis and localisation investigated using in situ hybridisation. We discuss significantly overrepresented functional ontology categories in the context of optic fissure morphogenesis and highlight interesting transcripts from hierarchical clustering for subsequent analysis. We have identified netrin1a ntn1a as highly differentially expressed across optic fissure fusion  with a resultant ocular coloboma phenotype following morpholino antisense translation blocking knockdown and downstream disruption of atoh7 expression. To support the identification of candidate genes in human studies  we have generated an online open access resource for fast and simple quantitative querying of the gene expression data. Our study represents the first comprehensive analysis of the zebrafish optic fissure transcriptome and provides a valuable resource to facilitate our understanding of the complex aetiology of ocular coloboma. Overall design: We used RNA seq to identify differentially expressed genes across optic fissure fusion in zebrafish. Samples were isolated retinal regions including the optic fissure OF region and control dorsal retina DR at timepoints; prefusion 32 hpf  fusing 48 hpf and post fusion 56 hpf. 5 biological replicates.", null, "pubmed:30733552;pubmed:35034853", null, "OF 48 hpf Rep1 [1 48 O]", "GSM4848058", null, "source name:optic fissure retina 48 hpf|hpf:48|tissue:optic fissure retina", "OF 48 hpf Rep1 [1 48 O]", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using trimgalore Reads were aligned to the genome and transcriptome using STAR v2.4.0 using parameters   outSAMtype BAM Unsorted   outSAMunmapped Within Resulting BAM files were sorted by coodinates and duplicates soft marked with picard MarkDuplicates Count files were created using htseq  count v0.6.1 and modelled using DESeq2 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw count values for each sample", "optic fissure retina 48 hpf", null, "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "zebrafish were harvested at appropriate time points hpf  retinal regions dissected", "hpf:48|tissue:optic fissure retina", "GSM4848058", "GSM4848058: OF 48 hpf Rep1 [1 48 O]; Danio rerio; RNA Seq", "GSM4848058", null, "1", "RNA was extracted using Qiagen Rneasy FFPE kit and quantified RNA seq libraries were constructed using the SMARTer low input  kit using standard protocols", "GEO Accession:GSM4848058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP288083", null, null, "1-48-O_R1.fastq.gz 1-48-O_R2.fastq.gz", "fastq fastq", 2552005400.0, 12760027.0, "GSM4848058 r1", "0:100 1:100", "A:720990425;C:556371737;G:577499015;T:694589372;N:2554851", 100, 100, null, null, 720990425, 556371737, 577499015, 694589372, 2554851, "SRX9340659", "SRS7562467", "SRA1146222", "GEO", "Institute of Ophthalmology, UCL", 2, 0.93333, 0.93374, 0.1828, 0.18383, 0.73708, 0.73841, 0.49612, 0.49916, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-10-21", "Hatching", "Embryo", "Eye", "Sensory System"], [69475, "SRR18712324", "SRX14812927", "SRS12569570", "SRP369458", "PRJNA825495", "Regulation of retina microexons by srrm3 in zebrafish", "PRJNA825495", "Other", "To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf  60 hpf  and 72 hpf larvae WT and KO for srrm3.", null, null, null, null, "Eye 60hpf WT b", null, "strain:WT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Eyes from 60 hpf larvae WT for the eMIC domain of srrm3.", "Eye 60hpf WT", "Eye 60hpf WT", "WT and srrm3 mutant zebrafish were grown at  28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP369458", null, null, "Eye_60hpf_WT_b_R1-125.fq.gz Eye_60hpf_WT_b_R2-125.fq.gz", "fastq fastq", 15250592500.0, 61002370.0, "Eye 60hpf WT b R1 125.fq.gz", "0:125 1:125", "A:3923837289;C:3702942025;G:3742033933;T:3872922356;N:8856897", 125, 125, null, null, 3923837289, 3702942025, 3742033933, 3872922356, 8856897, "SRX14812927", "SRS12569570", "SRA1402039", "Centre for Genomic Regulation|Systems Biology", "Centre for Genomic Regulation|Systems Biology", 2, 0.97168, 0.9731, 0.0527, 0.05258, 0.69891, 0.70041, 0.45973, 0.45381, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2022-04-11", "Hatching", "Embryo", "Eye", "Sensory System"], [69476, "SRR18712325", "SRX14812926", "SRS12569569", "SRP369458", "PRJNA825495", "Regulation of retina microexons by srrm3 in zebrafish", "PRJNA825495", "Other", "To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf  60 hpf  and 72 hpf larvae WT and KO for srrm3.", null, null, null, null, "Eye 60hpf MUT b", null, "strain:srrm3 MUT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Eyes from 60 hpf larvae mutated for the eMIC domain of srrm3.", "Eye 60hpf MUT", "Eye 60hpf MUT", "WT and srrm3 mutant zebrafish were grown at  28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP369458", null, null, "Eye_60hpf_MUT_b_R1-125.fq.gz Eye_60hpf_MUT_b_R2-125.fq.gz", "fastq fastq", 14932544250.0, 59730177.0, "Eye 60hpf MUT b R1 125.fq.gz", "0:125 1:125", "A:3891825609;C:3575114135;G:3598083383;T:3858808039;N:8713084", 125, 125, null, null, 3891825609, 3575114135, 3598083383, 3858808039, 8713084, "SRX14812926", "SRS12569569", "SRA1402039", "Centre for Genomic Regulation|Systems Biology", "Centre for Genomic Regulation|Systems Biology", 2, 0.96985, 0.97098, 0.06006, 0.0593, 0.68939, 0.6926, 0.46001, 0.45867, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2022-04-11", "Hatching", "Embryo", "Eye", "Sensory System"], [69477, "SRR18712326", "SRX14812925", "SRS12569568", "SRP369458", "PRJNA825495", "Regulation of retina microexons by srrm3 in zebrafish", "PRJNA825495", "Other", "To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf  60 hpf  and 72 hpf larvae WT and KO for srrm3.", null, null, null, null, "Eye 48hpf WT b", null, "strain:WT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Eyes from 48 hpf larvae WT for the eMIC domain of srrm3.", "Eye 48hpf WT", "Eye 48hpf WT", "WT and srrm3 mutant zebrafish were grown at  28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP369458", null, null, "Eye_48hpf_WT_b_R1-125.fq.gz Eye_48hpf_WT_b_R2-125.fq.gz", "fastq fastq", 15736041750.0, 62944167.0, "Eye 48hpf WT b R1 125.fq.gz", "0:125 1:125", "A:4076543478;C:3787178416;G:3834447099;T:4028745594;N:9127163", 125, 125, null, null, 4076543478, 3787178416, 3834447099, 4028745594, 9127163, "SRX14812925", "SRS12569568", "SRA1402039", "Centre for Genomic Regulation|Systems Biology", "Centre for Genomic Regulation|Systems Biology", 2, 0.97095, 0.97209, 0.05101, 0.05067, 0.69408, 0.69767, 0.47501, 0.47714, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2022-04-11", "Hatching", "Embryo", "Eye", "Sensory System"], [69478, "SRR18712327", "SRX14812924", "SRS12569567", "SRP369458", "PRJNA825495", "Regulation of retina microexons by srrm3 in zebrafish", "PRJNA825495", "Other", "To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf  60 hpf  and 72 hpf larvae WT and KO for srrm3.", null, null, null, null, "Eye 48hpf MUT b", null, "strain:srrm3 MUT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Eyes from 48 hpf larvae mutated for the eMIC domain of srrm3.", "Eye 48hpf MUT", "Eye 48hpf MUT", "WT and srrm3 mutant zebrafish were grown at  28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP369458", null, null, "Eye_48hpf_MUT_b_R1-125.fq.gz Eye_48hpf_MUT_b_R2-125.fq.gz", "fastq fastq", 14845531750.0, 59382127.0, "Eye 48hpf MUT b R1 125.fq.gz", "0:125 1:125", "A:3879709745;C:3539390575;G:3573173326;T:3844623832;N:8634272", 125, 125, null, null, 3879709745, 3539390575, 3573173326, 3844623832, 8634272, "SRX14812924", "SRS12569567", "SRA1402039", "Centre for Genomic Regulation|Systems Biology", "Centre for Genomic Regulation|Systems Biology", 2, 0.9684, 0.97006, 0.05578, 0.05498, 0.69183, 0.69581, 0.472, 0.46674, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2022-04-11", "Hatching", "Embryo", "Eye", "Sensory System"]], "truncated": false, "filtered_table_rows_count": 85, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Hatching", "p1": "Eye"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 65, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "cDNA", "label": "cDNA", "count": 58, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_selection=cDNA", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 27, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_selection=RANDOM", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 51, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 34, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "Embryo", "label": "Embryo", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "Hatching", "label": "Hatching", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Eye", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "Sensory System", "label": "Sensory System", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&tissue_curation_coarse=Sensory+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "Eye", "label": "Eye", "count": 85, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye", "results": [{"value": "unknown", "label": "unknown", "count": 40, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&technology=unknown", "selected": false}, {"value": "smartseq", "label": "smartseq", "count": 23, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&technology=smartseq", "selected": false}, {"value": "10x", "label": "10x", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Hatching&tissue_curation=Eye&technology=10x", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 72.13402599882102}