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94 rows where devstage_curation = "Pharyngula" and tissue_curation_coarse = "Sensory System"

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technology 4

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Sensory System · 94 ✖

tissue_curation 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Pharyngula · 94 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
19098 19098 ERR13822110 ERX13224862 ERS21098697 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR2 S2 R1 001.fastq.gz 38 PR2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR2 webin reads 38 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR2_S2_R1_001.fastq.gz fastq 3463281109.0 34821985.0 webin reads 38 PR2 0:99.46 A:969862466;C:733798241;G:755135957;T:1004440555;N:43890 99       969862466 733798241 755135957 1004440555 43890 ERX13224862 ERS21098697 ERA30879238 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19099 19099 ERR13822784 ERX13225536 ERS21098706 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC3 S11 R1 001.fastq.gz 38 HC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC3 webin reads 38 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC3_S11_R1_001.fastq.gz fastq 4360921873.0 44107486.0 webin reads 38 HC3 0:98.87 A:1222778761;C:918257887;G:948838973;T:1270939370;N:106882 98       1222778761 918257887 948838973 1270939370 106882 ERX13225536 ERS21098706 ERA30879613 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19103 19103 ERR13822197 ERX13224949 ERS21098704 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC1 S9 R1 001.fastq.gz SAMEA116100624 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 HC1 webin reads 38 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC1_S9_R1_001.fastq.gz fastq 3784641498.0 38331162.0 webin reads 38 HC1 0:98.74 A:1064199311;C:791310791;G:818910597;T:1110118632;N:102167 98       1064199311 791310791 818910597 1110118632 102167 ERX13224949 ERS21098704 ERA30879548 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19106 19106 ERR13822131 ERX13224883 ERS21098700 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC1 S5 R1 001.fastq.gz SAMEA116100620 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 AC1|collected by:Jaakko Lehtimaki|collection date:2021 11 30|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 AC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 AC1 webin reads 38 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC1_S5_R1_001.fastq.gz fastq 3836921113.0 38702139.0 webin reads 38 AC1 0:99.14 A:1066720805;C:818958589;G:843762182;T:1107403844;N:75693 99       1066720805 818958589 843762182 1107403844 75693 ERX13224883 ERS21098700 ERA30879356 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19107 19107 ERR13822143 ERX13224895 ERS21098702 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC3 S7 R1 001.fastq.gz 38 AC3   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC3 webin reads 38 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC3_S7_R1_001.fastq.gz fastq 3452707377.0 34902410.0 webin reads 38 AC3 0:98.92 A:970868997;C:726795179;G:750560378;T:1004408693;N:74130 98       970868997 726795179 750560378 1004408693 74130 ERX13224895 ERS21098702 ERA30879451 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19109 19109 ERR13822153 ERX13224905 ERS21098703 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC4 S8 R1 001.fastq.gz 38 AC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC4 webin reads 38 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC4_S8_R1_001.fastq.gz fastq 4130629624.0 41794865.0 webin reads 38 AC4 0:98.83 A:1156746387;C:877063962;G:905379690;T:1191264308;N:175277 98       1156746387 877063962 905379690 1191264308 175277 ERX13224905 ERS21098703 ERA30879532 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19110 19110 ERR13822201 ERX13224953 ERS21098705 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC2 S10 R1 001.fastq.gz 38 HC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC2 webin reads 38 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC2_S10_R1_001.fastq.gz fastq 4221340137.0 42584743.0 webin reads 38 HC2 0:99.13 A:1195817135;C:879958039;G:908085464;T:1237394738;N:84761 99       1195817135 879958039 908085464 1237394738 84761 ERX13224953 ERS21098705 ERA30879582 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19111 19111 ERR13822114 ERX13224866 ERS21098698 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR3 S3 R1 001.fastq.gz SAMEA116100618 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:38 PR3|collected by:Jaakko Lehtimaki|collection date:2021 12 07|common name:zebrafish|dev stage:38 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:38 PR3|scientific name:Danio rerio|tissue type:retina                 Raw reads: 38 PR3 webin reads 38 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR3_S3_R1_001.fastq.gz fastq 3894010106.0 39196855.0 webin reads 38 PR3 0:99.34 A:1093221995;C:818047738;G:843661747;T:1138957138;N:121488 99       1093221995 818047738 843661747 1138957138 121488 ERX13224866 ERS21098698 ERA30879273 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Pharyngula Embryo Eye Sensory System
19112 19112 ERR13822135 ERX13224887 ERS21098701 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38AC2 S6 R1 001.fastq.gz 38 AC2   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 AC2 webin reads 38 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38AC2_S6_R1_001.fastq.gz fastq 3913343007.0 39682834.0 webin reads 38 AC2 0:98.62 A:1089960083;C:827936673;G:855955684;T:1139372607;N:117960 98       1089960083 827936673 855955684 1139372607 117960 ERX13224887 ERS21098701 ERA30879382 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19115 19115 ERR13822099 ERX13224851 ERS21098696 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR1 S1 R1 001.fastq.gz 38 PR1   organism:Danio rerio|collection date:2021 11 30|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR1 webin reads 38 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR1_S1_R1_001.fastq.gz fastq 4256158288.0 42658127.0 webin reads 38 PR1 0:99.77 A:1193880575;C:899261652;G:926114030;T:1236860186;N:41845 99       1193880575 899261652 926114030 1236860186 41845 ERX13224851 ERS21098696 ERA30879152 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19116 19116 ERR13822119 ERX13224871 ERS21098699 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38PR4 S4 R1 001.fastq.gz 38 PR4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 PR4 webin reads 38 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38PR4_S4_R1_001.fastq.gz fastq 3726308046.0 37591038.0 webin reads 38 PR4 0:99.13 A:1043231302;C:789255840;G:812957881;T:1080801843;N:61180 99       1043231302 789255840 812957881 1080801843 61180 ERX13224871 ERS21098699 ERA30879302 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
19120 19120 ERR13822788 ERX13225540 ERS21098707 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 38HC4 S12 R1 001.fastq.gz 38 HC4   organism:Danio rerio|collection date:2021 12 07|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:38 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 38 HC4 webin reads 38 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 38 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 38HC4_S12_R1_001.fastq.gz fastq 3353994440.0 33744828.0 webin reads 38 HC4 0:99.39 A:939537209;C:709367668;G:731849729;T:973193819;N:46015 99       939537209 709367668 731849729 973193819 46015 ERX13225540 ERS21098707 ERA30879650 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Pharyngula Embryo Eye Sensory System
39795 39795 SRR2145848 SRX1133838 SRS1023794 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   YapS87A rep3 GSM1844492   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A YapS87A rep3 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A GSM1844492 GSM1844492: YapS87A rep3; Danio rerio; RNA Seq GSM1844492   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844492 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     YapS87A_3_sequence.txt.gz fastq 1680502581.0 32951031.0 GSM1844492 r1 0:51 A:431882743;C:376993099;G:378520286;T:464147117;N:28959336 51       431882743 376993099 378520286 464147117 28959336 SRX1133838 SRS1023794 SRA282186 GEO Medical College of Wisconsin 1 0.9063   0.08492   0.73279   0.45445   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
39796 39796 SRR2145847 SRX1133837 SRS1023795 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   YapS87A rep2 GSM1844491   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A YapS87A rep2 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A GSM1844491 GSM1844491: YapS87A rep2; Danio rerio; RNA Seq GSM1844491   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844491 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     YapS87A_2_sequence.txt.gz fastq 1742004705.0 34156955.0 GSM1844491 r1 0:51 A:447373634;C:393295480;G:396777263;T:483090843;N:21467485 51       447373634 393295480 396777263 483090843 21467485 SRX1133837 SRS1023795 SRA282186 GEO Medical College of Wisconsin 1 0.90563   0.0858   0.72707   0.46494   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
39797 39797 SRR2145846 SRX1133836 SRS1023796 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   YapS87A rep1 GSM1844490   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A YapS87A rep1 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4/dsRed:14xUAS:YapS87A GSM1844490 GSM1844490: YapS87A rep1; Danio rerio; RNA Seq GSM1844490   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844490 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     YapS87A_1_sequence.txt.gz fastq 1605602451.0 31482401.0 GSM1844490 r1 0:51 A:416296166;C:357147049;G:359581538;T:444847570;N:27730128 51       416296166 357147049 359581538 444847570 27730128 SRX1133836 SRS1023796 SRA282186 GEO Medical College of Wisconsin 1 0.90209   0.08942   0.72979   0.47171   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
39798 39798 SRR2145845 SRX1133835 SRS1023797 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   WT rep3 GSM1844489   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control WT rep3 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control GSM1844489 GSM1844489: WT rep3; Danio rerio; RNA Seq GSM1844489   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844489 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     WT_3_sequence.txt.gz fastq 1609588305.0 31560555.0 GSM1844489 r1 0:51 A:412663150;C:358619332;G:364439350;T:446055681;N:27810792 51       412663150 358619332 364439350 446055681 27810792 SRX1133835 SRS1023797 SRA282186 GEO Medical College of Wisconsin 1 0.92186   0.07797   0.73499   0.47006   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
39799 39799 SRR2145844 SRX1133834 SRS1023798 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   WT rep2 GSM1844488   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control WT rep2 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control GSM1844488 GSM1844488: WT rep2; Danio rerio; RNA Seq GSM1844488   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844488 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     WT_2_sequence.txt.gz fastq 1637145594.0 32100894.0 GSM1844488 r1 0:51 A:414176151;C:369403072;G:372539483;T:452762354;N:28264534 51       414176151 369403072 372539483 452762354 28264534 SRX1133834 SRS1023798 SRA282186 GEO Medical College of Wisconsin 1 0.92352   0.08166   0.7318   0.47492   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
39800 39800 SRR2145843 SRX1133833 SRS1023799 SRP062048 PRJNA291981 Yap and Taz regulate retinal pigment epithelial cell fate GSE71681 Transcriptome Analysis The optic vesicle comprises a pool of bi potential progenitor cells from which the retinal pigment epithelium RPE and neural retina fates segregate during ocular morphogenesis. Several transcription factors and signaling pathways have been shown to be important for RPE maintenance and differentiation but an understanding of the initial fate specification and determination of this ocular cell type is lacking. We show that Yap/Taz Tead activity is necessary and sufficient for optic vesicle progenitors to adopt RPE identity in zebrafish. A Teadresponsive transgene is expressed within the domain of the optic cup from which RPE arises and Yap immunoreactivity localizes to the nuclei of prospective RPE cells. yap yap1 mutants lack a subset of RPE cells and/or exhibit coloboma. Loss of RPE in yap mutants is exacerbated in combination with taz wwtr1 mutant alleles such that when Yap and Taz are both absent optic vesicle progenitor cells completely lose their ability to form RPE. The mechanism of Yap dependent RPE cell type determination is reliant on both nuclear localization of Yap and interaction with a Tead co factor. In contrast to loss of Yap and Taz overexpression of either protein within optic vesicle progenitors leads to ectopic pigmentation in a dosagedependent manner. Overall this study identifies Yap and Taz as key early regulators of RPE genesis and provides a mechanistic framework for understanding the congenital ocular defects of Sveinsson’s chorioretinal atrophy and congenital retinal coloboma. Overall design: 60 pooled eyes from 36 hpf wild type or vsx2:Gal4/dsRed:14xUAS:YapS87A embryos were pooled for one sample. Three wild type and three vsx2:Gal4/dsRed:14xUAS:YapS87A pools were analyzed for RNA.   pubmed:26209646   WT rep1 GSM1844487   source name:whole eye|developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control WT rep1 RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. 30M reads per sample Genome build: Danio rerio EnsEMBL release 66. Supplementary files format and content: tab delimited txt include fkpm for each sample. whole eye   Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66.   developmental stage:36 hpf|tissue:whole eye|genotype:vsx2:Gal4 sibling control GSM1844487 GSM1844487: WT rep1; Danio rerio; RNA Seq GSM1844487   1 Yap S87A and sibling control whole eyes were dissected at 36 hpf and immediately frozen on dry ice until 60 pooled retinas were obtained for each genotype. RNA was purified as described in Uribe et al. 2012 except that RNA was eluted in a 50μl final volume. RNA quality was determined using an Agilent BioAnalyzer. 50 bp single read sequencing was performed in triplicate for each genotype using an Illumina HiSeq2000 at VANTAGE Vanderbilt University Nashville TN. Sequencing results were analyzed by VANGARD Vanderbilt University Nashville TN. RNA seq reads were mapped to D. rerio cDNA sequences from EnsEMBL release 66. GEO Accession:GSM1844487 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP062048     WT_1_sequence.txt.gz fastq 1666445961.0 32675411.0 GSM1844487 r1 0:51 A:421437796;C:380026405;G:379400332;T:465027467;N:20553961 51       421437796 380026405 379400332 465027467 20553961 SRX1133833 SRS1023799 SRA282186 GEO Medical College of Wisconsin 1 0.91935   0.0764   0.73083   0.47263   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   United States 2015-08-05 Pharyngula Embryo Eye Sensory System
40749 40749 SRR5398205 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S3A_L001_R1_001.fastq.gz Tet23_WT_S3A_L001_R2_001.fastq.gz fastq fastq 1736290800.0 11575272.0 GSM2560112 r1 0:75 1:75 A:463866065;C:394401152;G:421273078;T:456696859;N:53646 75 75     463866065 394401152 421273078 456696859 53646 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95212 0.95456 0.08517 0.08502 0.73133 0.7359 0.49341 0.49384 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40750 40750 SRR5398206 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S3A_L002_R1_001.fastq.gz Tet23_WT_S3A_L002_R2_001.fastq.gz fastq fastq 1696221750.0 11308145.0 GSM2560112 r2 0:75 1:75 A:456170554;C:387128779;G:404135089;T:448752581;N:34747 75 75     456170554 387128779 404135089 448752581 34747 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95272 0.95484 0.08501 0.08449 0.73202 0.73716 0.48838 0.49326 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40751 40751 SRR5398207 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S3A_L003_R1_001.fastq.gz Tet23_WT_S3A_L003_R2_001.fastq.gz fastq fastq 1748587500.0 11657250.0 GSM2560112 r3 0:75 1:75 A:468993983;C:399108810;G:419724835;T:460692327;N:67545 75 75     468993983 399108810 419724835 460692327 67545 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95297 0.95521 0.08451 0.0842 0.73099 0.73547 0.48891 0.49776 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40752 40752 SRR5398208 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S3A_L004_R1_001.fastq.gz Tet23_WT_S3A_L004_R2_001.fastq.gz fastq fastq 1765673250.0 11771155.0 GSM2560112 r4 0:75 1:75 A:475717971;C:403009973;G:419549330;T:467351495;N:44481 75 75     475717971 403009973 419549330 467351495 44481 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95279 0.95464 0.08609 0.08547 0.73068 0.73537 0.49079 0.49222 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40753 40753 SRR5398209 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S2B_L001_R1_001.fastq.gz Tet23_WT_S2B_L001_R2_001.fastq.gz fastq fastq 2398792200.0 15991948.0 GSM2560112 r5 0:75 1:75 A:638883536;C:543595407;G:587119220;T:629186766;N:7271 75 75     638883536 543595407 587119220 629186766 7271 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95164 0.95332 0.08547 0.08571 0.73314 0.73703 0.49888 0.4984 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40754 40754 SRR5398210 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S2B_L002_R1_001.fastq.gz Tet23_WT_S2B_L002_R2_001.fastq.gz fastq fastq 2431408200.0 16209388.0 GSM2560112 r6 0:75 1:75 A:647420622;C:550083443;G:598370298;T:635524808;N:9029 75 75     647420622 550083443 598370298 635524808 9029 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95256 0.95232 0.086 0.08428 0.73304 0.73882 0.49207 0.48822 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40755 40755 SRR5398211 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S2B_L003_R1_001.fastq.gz Tet23_WT_S2B_L003_R2_001.fastq.gz fastq fastq 2579844600.0 17198964.0 GSM2560112 r7 0:75 1:75 A:682865856;C:584532060;G:638175727;T:674119204;N:151753 75 75     682865856 584532060 638175727 674119204 151753 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95198 0.95295 0.08327 0.08238 0.73087 0.73614 0.49484 0.49177 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40756 40756 SRR5398212 SRX2692999 SRS2089612 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   sibling at 36hpf GSM2560112   source name:whole eye tissue|strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf sibling at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:sibling control|tissue:dissected eyes|age:36 hpf GSM2560112 GSM2560112: sibling at 36hpf; Danio rerio; RNA Seq GSM2560112   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560112 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_WT_S2B_L004_R1_001.fastq.gz Tet23_WT_S2B_L004_R2_001.fastq.gz fastq fastq 2527779000.0 16851860.0 GSM2560112 r8 0:75 1:75 A:667174371;C:572028335;G:630346069;T:658063231;N:166994 75 75     667174371 572028335 630346069 658063231 166994 SRX2692999 SRS2089612 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95204 0.95131 0.08427 0.08315 0.7321 0.73693 0.49314 0.48924 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40757 40757 SRR5398197 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S2A_L001_R1_001.fastq.gz Tet23_mut_S2A_L001_R2_001.fastq.gz fastq fastq 1808238300.0 12054922.0 GSM2560111 r1 0:75 1:75 A:478777075;C:415526446;G:442420917;T:471456996;N:56866 75 75     478777075 415526446 442420917 471456996 56866 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95228 0.95465 0.08154 0.08069 0.7251 0.72823 0.47948 0.49681 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40758 40758 SRR5398198 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S2A_L002_R2_001.fastq.gz Tet23_mut_S2A_L002_R1_001.fastq.gz fastq fastq 1761504900.0 11743366.0 GSM2560111 r2 0:75 1:75 A:469860774;C:407250899;G:421722817;T:462635873;N:34537 75 75     469860774 407250899 421722817 462635873 34537 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95298 0.95502 0.08099 0.08071 0.72484 0.72876 0.47709 0.48781 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40759 40759 SRR5398199 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S2A_L003_R1_001.fastq.gz Tet23_mut_S2A_L003_R2_001.fastq.gz fastq fastq 1822166550.0 12147777.0 GSM2560111 r3 0:75 1:75 A:484551750;C:421085869;G:440333372;T:476125942;N:69617 75 75     484551750 421085869 440333372 476125942 69617 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95319 0.95596 0.08072 0.08003 0.72521 0.72902 0.47768 0.4867 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40760 40760 SRR5398200 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S2A_L004_R2_001.fastq.gz Tet23_mut_S2A_L004_R1_001.fastq.gz fastq fastq 1833637500.0 12224250.0 GSM2560111 r4 0:75 1:75 A:490037145;C:424073634;G:437471367;T:482010327;N:45027 75 75     490037145 424073634 437471367 482010327 45027 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95266 0.95539 0.08238 0.0817 0.72577 0.72953 0.48057 0.49993 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40761 40761 SRR5398201 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S1B_L001_R2_001.fastq.gz Tet23_mut_S1B_L001_R1_001.fastq.gz fastq fastq 3134111700.0 20894078.0 GSM2560111 r5 0:75 1:75 A:827074933;C:718072178;G:774455494;T:814499468;N:9627 75 75     827074933 718072178 774455494 814499468 9627 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95252 0.95355 0.0819 0.08114 0.72656 0.73221 0.48668 0.49637 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40762 40762 SRR5398202 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S1B_L002_R2_001.fastq.gz Tet23_mut_S1B_L002_R1_001.fastq.gz fastq fastq 3175850400.0 21172336.0 GSM2560111 r6 0:75 1:75 A:837531545;C:726292618;G:789503776;T:822510973;N:11488 75 75     837531545 726292618 789503776 822510973 11488 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95254 0.95249 0.08229 0.08163 0.72606 0.73156 0.48458 0.49767 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40763 40763 SRR5398203 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S1B_L003_R2_001.fastq.gz Tet23_mut_S1B_L003_R1_001.fastq.gz fastq fastq 3370638450.0 22470923.0 GSM2560111 r7 0:75 1:75 A:883731406;C:771558378;G:842531443;T:872613847;N:203376 75 75     883731406 771558378 842531443 872613847 203376 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95286 0.95228 0.08072 0.07947 0.72478 0.72941 0.48264 0.48603 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
40764 40764 SRR5398204 SRX2692998 SRS2089611 SRP073099 PRJNA318016 Tet mediated DNA hydroxymethylation regulates retinal neurogenesis in zebrafish via cell extrinsic signaling pathways GSE80134 Transcriptome Analysis Using zebrafish tet2 / ;tet3 / mutants we identify functions for Tet enzymes and 5 hydroxymethylcytosine 5hmC in regulating gene expression and cell type specific differentiation during retinal development. Overall design: RNAseq from tet2 / ;tet3 / mutant and sibling embryonic eye tissues dissected at 72hpf and 36hpf.   pubmed:28926578   tet2 / ;tet3 / mutants at 36hpf GSM2560111   source name:whole eye tissue|strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf tet2 / ;tet3 / mutants at 36hpf base calling demultiplexing done at University of Pittsburgh Genomic Research Core fastq files quality checked using FastQC mapped using CLC Genomics Grid Worker 7.5.1 gene counting and differentially expressed genes identified using CLC Genomics Grid Worker 7.5.1 Genome build: GRCz10 Supplementary files format and content: Tet23 36hpf GE all.xlsx whole eye tissue none whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. zebrafish embryos raised under standard condition strain:TL|genotype/variation:tet2 / ;tet3 / mutants|tissue:dissected eyes|age:36 hpf GSM2560111 GSM2560111: tet2 / ;tet3 / mutants at 36hpf; Danio rerio; RNA Seq GSM2560111   1 whole eyes were dissected from fresh euthanized embryos. RNA immediately extracted using TriZol and QIAGEN RNeasy mini columns following manufacturer's protocol RNA samples were processed for RNAseq using Ambion poly A capture kit and NEB Next kit for cDNA synthesis and library prep. GEO Accession:GSM2560111 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP073099     Tet23_mut_S1B_L004_R2_001.fastq.gz Tet23_mut_S1B_L004_R1_001.fastq.gz fastq fastq 3302704350.0 22018029.0 GSM2560111 r8 0:75 1:75 A:863198737;C:754978257;G:832631367;T:851679478;N:216511 75 75     863198737 754978257 832631367 851679478 216511 SRX2692998 SRS2089611 SRA409011 GEO Gross, Ophthalmology, University of Pittsburgh 2 0.95204 0.95116 0.08067 0.07961 0.7263 0.73044 0.47664 0.49378 75 75 B B biological fallback assumption illumina nextseq unknown poly_a nebnext bulk unknown unknown   United States 2017-03-30 Pharyngula Embryo Eye Sensory System
50662 50662 SRR8206453 SRX5025778 SRS4057278 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   pubmed:32467236   36 hpf retina GSM3478014   source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:36 hpf 36 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   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 40μm 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.   strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:36 hpf GSM3478014 GSM3478014: 36 hpf retina; Danio rerio; RNA Seq GSM3478014   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 40μm 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:GSM3478014 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP169565     36hpf_possorted_genome_bam.bam 10X Genomics bam file 55066871015.0 364681265.0 GSM3478014 r1 0:151 A:16004920970;C:11846723571;G:11830068402;T:15383410377;N:1747695 151       16004920970 11846723571 11830068402 15383410377 1747695 SRX5025778 SRS4057278 SRA812747 GEO Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS 1 0.86264   0.06425   0.83834   0.48474   151   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-11-19 Pharyngula Embryo Eye Sensory System
50663 50663 SRR8206452 SRX5025777 SRS4057277 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   pubmed:32467236   24 hpf retina GSM3478013   source name:Retina|strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:24 hpf 24 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   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 40μm 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.   strain:AB|genotype:wildtype|tissue:whole retina|developmental stage:24 hpf GSM3478013 GSM3478013: 24 hpf retina; Danio rerio; RNA Seq GSM3478013   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 40μm 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:GSM3478013 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP169565     24hpf_possorted_genome_bam.bam 10X Genomics bam file 64649431883.0 428141933.0 GSM3478013 r1 0:151 A:18206375554;C:14387069686;G:14012075221;T:18041887869;N:2023553 151       18206375554 14387069686 14012075221 18041887869 2023553 SRX5025777 SRS4057277 SRA812747 GEO Lab of Stem Cell and Neurogenesis, Institute of Neuroscience, CAS 1 0.88151   0.05606   0.8369   0.50733   151   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2018-11-19 Pharyngula Embryo Eye Sensory System
59292 59292 SRR11811475 SRX8362742 SRS6678633 SRP262311 PRJNA633835 Single cell RNA seq and ATAC seq of zebrafish retina GSE150839 Other To study the transcriptomic and chromatin accessibility heterogeneity of zebrafish retinal progenitor cells Overall design: 2 retinal samples from embryonic zebrafish   pubmed:32699896   RNA seq retina atoh7 44hpf GSM4559534   source name:retina|strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf RNA seq retina atoh7 44hpf Raw datasets of single cell RNA seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger software v2.1.0 10x Genomics to generate the processed matrix data. Raw data of single cell ATAC seq were aligned zebrafish genome GRCz10 filtered and counted using the Cell Ranger ATAC software v1.1 10x Genomics to generated the processed matrix data. Genome build: GRCz10 Supplementary files format and content: Processed data files are in tar.gz format containing matrix files for further analysis. retina   Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer’s protocol   strain:Tgatoh7:turboGFP dest1::atoh7:gapRFP|tissue:retina|developmental stage:44 hpf GSM4559534 GSM4559534: RNA seq retina atoh7 44hpf; Danio rerio; RNA Seq GSM4559534   1 Zebrafish retina at the desired developmental stages were dissected and dissociated using papain for single cell RNA seq. The single nuclei were further extracted by digitonin for single cell ATAC seq. The libraries were constructed using the Chromium Single Cell three prime Library &Gel Bead kit v2 Chip kit 10x genomics PN 120237 or the Chromium Single Cell ATAC Library & Gel Bead Kit 10x genomics following the manufacturer's protocol GEO Accession:GSM4559534 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP262311   intentional duplicate|options: max err count 100000000 atoh7_scRNA_bam.bam 10X Genomics bam file 61111212107.0 414028035.0 GSM4559534 r1 0:147.60 A:18052310869;C:12727112571;G:14225357068;T:16105981406;N:450193 147       18052310869 12727112571 14225357068 16105981406 450193 SRX8362742 SRS6678633 SRA1077074 GEO Institute of Neuroscience, Chinese Academy of Sciences 1 0.89647   0.06712   0.85228   0.50102   150   B   usable mapping rate illumina novaseq_era unknown cdna_unspecified unknown sc single_cell_droplet 10x   China 2020-05-19 Pharyngula Embryo Eye Sensory System
60457 60457 SRR12287401 SRX8790734 SRS7059126 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3 GSM4681961   source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:Torrin|age:36hpf|tissue:eyes GSM4681961 GSM4681961: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 3; Danio rerio; RNA Seq GSM4681961   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681961 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Tor_3.fq fastq 611438450.0 12228769.0 GSM4681961 r1 0:50 A:155737074;C:142979561;G:143702101;T:169019714;N:0 50       155737074 142979561 143702101 169019714 0 SRX8790734 SRS7059126 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.96219   0.1228   0.73219   0.50697   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60458 60458 SRR12287400 SRX8790733 SRS7059125 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2 GSM4681960   source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:Torrin|age:36hpf|tissue:eyes GSM4681960 GSM4681960: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 2; Danio rerio; RNA Seq GSM4681960   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681960 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Tor_2.fq fastq 610161700.0 12203234.0 GSM4681960 r1 0:50 A:153768852;C:143410611;G:145248964;T:167733273;N:0 50       153768852 143410611 145248964 167733273 0 SRX8790733 SRS7059125 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.96418   0.12127   0.73521   0.50591   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60459 60459 SRR12287399 SRX8790732 SRS7059124 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1 GSM4681959   source name:36hpf zebrafish eyes|treatment:Torrin|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:Torrin|age:36hpf|tissue:eyes GSM4681959 GSM4681959: 36hpf zebrafish eyes; Inhibition of mTOR signaling by Torrin; replicate 1; Danio rerio; RNA Seq GSM4681959   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681959 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Tor_1.fq fastq 568616650.0 11372333.0 GSM4681959 r1 0:50 A:143342391;C:133596830;G:136056983;T:155620446;N:0 50       143342391 133596830 136056983 155620446 0 SRX8790732 SRS7059124 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.96423   0.1166   0.73811   0.50869   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60460 60460 SRR12287398 SRX8790731 SRS7059123 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3 GSM4681958   source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:DMSO control|age:36hpf|tissue:eyes GSM4681958 GSM4681958: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 3; Danio rerio; RNA Seq GSM4681958   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681958 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     DMSO_3.fq fastq 710747750.0 14214955.0 GSM4681958 r1 0:50 A:184360596;C:160789051;G:160903077;T:204668511;N:26515 50       184360596 160789051 160903077 204668511 26515 SRX8790731 SRS7059123 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92693   0.14102   0.74233   0.52477   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60461 60461 SRR12287397 SRX8790730 SRS7059122 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2 GSM4681957   source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:DMSO control|age:36hpf|tissue:eyes GSM4681957 GSM4681957: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 2; Danio rerio; RNA Seq GSM4681957   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681957 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     DMSO_2.fq fastq 710470350.0 14209407.0 GSM4681957 r1 0:50 A:180578463;C:165554366;G:164357951;T:199952943;N:26627 50       180578463 165554366 164357951 199952943 26627 SRX8790730 SRS7059122 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92993   0.12326   0.73316   0.50795   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60462 60462 SRR12287396 SRX8790729 SRS7059121 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1 GSM4681956   source name:36hpf zebrafish eyes|treatment:DMSO control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   treatment:DMSO control|age:36hpf|tissue:eyes GSM4681956 GSM4681956: 36hpf zebrafish eyes; DMSO control for Torrin experiments; replicate 1; Danio rerio; RNA Seq GSM4681956   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681956 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     DMSO_1.fq fastq 684145550.0 13682911.0 GSM4681956 r1 0:50 A:176031808;C:157711101;G:157012646;T:193364628;N:25367 50       176031808 157711101 157012646 193364628 25367 SRX8790729 SRS7059121 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.93134   0.11826   0.73742   0.51639   50   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60463 60463 SRR12287395 SRX8790728 SRS7059120 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3 GSM4681955   source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes GSM4681955 GSM4681955: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 3; Danio rerio; RNA Seq GSM4681955   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681955 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Wnt2b_3.fq fastq 1683174573.0 33003423.0 GSM4681955 r1 0:51 A:425533518;C:379417030;G:382377050;T:466758495;N:29088480 51       425533518 379417030 382377050 466758495 29088480 SRX8790728 SRS7059120 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92087   0.07926   0.72699   0.50196   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60464 60464 SRR12287394 SRX8790727 SRS7059119 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2 GSM4681954   source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes GSM4681954 GSM4681954: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 2; Danio rerio; RNA Seq GSM4681954   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681954 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Wnt2b_2.fq fastq 1491166815.0 29238565.0 GSM4681954 r1 0:51 A:378958250;C:335771876;G:337239729;T:413432220;N:25764740 51       378958250 335771876 337239729 413432220 25764740 SRX8790727 SRS7059119 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92209   0.08083   0.733   0.51077   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60465 60465 SRR12287393 SRX8790726 SRS7059118 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1 GSM4681953   source name:36hpf zebrafish eyes|genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Wnt2ba overexpression|age:36hpf|tissue:eyes GSM4681953 GSM4681953: 36hpf zebrafish eyes; vsx2:Gal4>>Wnt2b replicate 1; Danio rerio; RNA Seq GSM4681953   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681953 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Wnt2b_1.fq fastq 1919112507.0 37629657.0 GSM4681953 r1 0:51 A:477418936;C:433410513;G:453965639;T:530637937;N:23679482 51       477418936 433410513 453965639 530637937 23679482 SRX8790726 SRS7059118 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.78015   0.06857   0.73608   0.49023   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60466 60466 SRR12287392 SRX8790725 SRS7059117 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   YapS87A replicate3 GSM4681952   source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes YapS87A replicate3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:YapS87A overexpression|age:36hpf|tissue:eyes GSM4681952 GSM4681952: YapS87A replicate3; Danio rerio; RNA Seq GSM4681952   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681952 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     YapS87A_3_sequence.txt fastq 1680502581.0 32951031.0 GSM4681952 r1 0:51 A:431882743;C:376993099;G:378520286;T:464147117;N:28959336 51       431882743 376993099 378520286 464147117 28959336 SRX8790725 SRS7059117 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.9063   0.08494   0.73308   0.45344   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60467 60467 SRR12287391 SRX8790724 SRS7059116 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   YapS87A replicate2 GSM4681951   source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes YapS87A replicate2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:YapS87A overexpression|age:36hpf|tissue:eyes GSM4681951 GSM4681951: YapS87A replicate2; Danio rerio; RNA Seq GSM4681951   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681951 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     YapS87A_2_sequence.txt fastq 1742004705.0 34156955.0 GSM4681951 r1 0:51 A:447373634;C:393295480;G:396777263;T:483090843;N:21467485 51       447373634 393295480 396777263 483090843 21467485 SRX8790724 SRS7059116 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90564   0.08572   0.72721   0.46483   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60468 60468 SRR12287390 SRX8790723 SRS7059115 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   YapS87A replicate1 GSM4681950   source name:36hpf zebrafish eyes|genotype:YapS87A overexpression|age:36hpf|tissue:eyes YapS87A replicate1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:YapS87A overexpression|age:36hpf|tissue:eyes GSM4681950 GSM4681950: YapS87A replicate1; Danio rerio; RNA Seq GSM4681950   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681950 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     YapS87A_1_sequence.txt fastq 1605602451.0 31482401.0 GSM4681950 r1 0:51 A:416296166;C:357147049;G:359581538;T:444847570;N:27730128 51       416296166 357147049 359581538 444847570 27730128 SRX8790723 SRS7059115 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90205   0.08929   0.72949   0.47221   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60469 60469 SRR12287389 SRX8790722 SRS7059114 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3 GSM4681949   source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes GSM4681949 GSM4681949: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate3; Danio rerio; RNA Seq GSM4681949   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681949 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     WT_3_sequence.txt fastq 1609588305.0 31560555.0 GSM4681949 r1 0:51 A:412663150;C:358619332;G:364439350;T:446055681;N:27810792 51       412663150 358619332 364439350 446055681 27810792 SRX8790722 SRS7059114 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92187   0.07809   0.73517   0.46998   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60470 60470 SRR12287388 SRX8790721 SRS7059113 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2 GSM4681948   source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes GSM4681948 GSM4681948: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate2; Danio rerio; RNA Seq GSM4681948   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681948 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     WT_2_sequence.txt fastq 1637145594.0 32100894.0 GSM4681948 r1 0:51 A:414176151;C:369403072;G:372539483;T:452762354;N:28264534 51       414176151 369403072 372539483 452762354 28264534 SRX8790721 SRS7059113 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92354   0.08166   0.73174   0.47515   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60471 60471 SRR12287387 SRX8790720 SRS7059112 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1 GSM4681947   source name:36hpf zebrafish eyes|genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Gal4 Control for Wnt2b and YapS87A|age:36hpf|tissue:eyes GSM4681947 GSM4681947: 36hpf zebrafish eyes; WT control for Wnt2b experiments; replicate1; Danio rerio; RNA Seq GSM4681947   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681947 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     WT_1_sequence.txt fastq 1666445961.0 32675411.0 GSM4681947 r1 0:51 A:421437796;C:380026405;G:379400332;T:465027467;N:20553961 51       421437796 380026405 379400332 465027467 20553961 SRX8790720 SRS7059112 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91939   0.07636   0.73052   0.4731   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60472 60472 SRR12287386 SRX8790719 SRS7059111 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3 GSM4681946   source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD overexpression|age:36hpf|tissue:eyes GSM4681946 GSM4681946: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 3; Danio rerio; RNA Seq GSM4681946   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681946 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_3.fq fastq 1687493202.0 33088102.0 GSM4681946 r1 0:51 A:466000780;C:363861781;G:362676818;T:465728464;N:29225359 51       466000780 363861781 362676818 465728464 29225359 SRX8790719 SRS7059111 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90234   0.10242   0.71488   0.47661   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60473 60473 SRR12287385 SRX8790718 SRS7059110 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2 GSM4681945   source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD overexpression|age:36hpf|tissue:eyes GSM4681945 GSM4681945: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 2; Danio rerio; RNA Seq GSM4681945   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681945 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_2.fq fastq 1724098248.0 33805848.0 GSM4681945 r1 0:51 A:479329096;C:373215849;G:370751023;T:475738259;N:25064021 51       479329096 373215849 370751023 475738259 25064021 SRX8790718 SRS7059110 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90041   0.1068   0.71571   0.48007   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60474 60474 SRR12287384 SRX8790717 SRS7059109 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1 GSM4681944   source name:36hpf zebrafish eyes|genotype:NICD overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD overexpression|age:36hpf|tissue:eyes GSM4681944 GSM4681944: 36hpf zebrafish eyes; vsx2:Gal4>>NICD1a replicate 1; Danio rerio; RNA Seq GSM4681944   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681944 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_1.fq fastq 1929410682.0 37831582.0 GSM4681944 r1 0:51 A:531140272;C:421394845;G:418288095;T:530541126;N:28046344 51       531140272 421394845 418288095 530541126 28046344 SRX8790717 SRS7059109 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90898   0.10574   0.71898   0.47601   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60475 60475 SRR12287383 SRX8790716 SRS7059108 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6 GSM4681943   source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD Control|age:36hpf|tissue:eyes GSM4681943 GSM4681943: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 6; Danio rerio; RNA Seq GSM4681943   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681943 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_Control_6.fq fastq 2023785927.0 39682077.0 GSM4681943 r1 0:51 A:561742336;C:444105929;G:439290439;T:558958186;N:19689037 51       561742336 444105929 439290439 558958186 19689037 SRX8790716 SRS7059108 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91779   0.10376   0.72468   0.46199   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60476 60476 SRR12287382 SRX8790715 SRS7059107 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5 GSM4681942   source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD Control|age:36hpf|tissue:eyes GSM4681942 GSM4681942: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 5; Danio rerio; RNA Seq GSM4681942   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681942 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_Control_5.fq fastq 1740124386.0 34120086.0 GSM4681942 r1 0:51 A:465085934;C:391698178;G:386868685;T:479536883;N:16934706 51       465085934 391698178 386868685 479536883 16934706 SRX8790715 SRS7059107 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.92122   0.09508   0.72606   0.47404   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60477 60477 SRR12287381 SRX8790714 SRS7059106 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1 GSM4681941   source name:36hpf zebrafish eyes|genotype:NICD Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:NICD Control|age:36hpf|tissue:eyes GSM4681941 GSM4681941: 36hpf zebrafish eyes; Gal4 control for NICD experiments; replicate 1; Danio rerio; RNA Seq GSM4681941   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681941 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     NICD_Control_1.fq fastq 1876256595.0 36789345.0 GSM4681941 r1 0:51 A:505568821;C:417420484;G:410313801;T:515696712;N:27256777 51       505568821 417420484 410313801 515696712 27256777 SRX8790714 SRS7059106 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91459   0.09419   0.72512   0.46824   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60478 60478 SRR12287380 SRX8790713 SRS7059105 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3 GSM4681940   source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes GSM4681940 GSM4681940: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 3; Danio rerio; RNA Seq GSM4681940   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681940 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_3.fq fastq 1937833026.0 37996726.0 GSM4681940 r1 0:51 A:519376884;C:429809002;G:419678420;T:530881829;N:38086891 51       519376884 429809002 419678420 530881829 38086891 SRX8790713 SRS7059105 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.9087   0.1008   0.72705   0.47617   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60479 60479 SRR12287379 SRX8790712 SRS7059104 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2 GSM4681939   source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes GSM4681939 GSM4681939: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 2; Danio rerio; RNA Seq GSM4681939   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681939 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_2.fq fastq 1538149392.0 30159792.0 GSM4681939 r1 0:51 A:404899388;C:344011831;G:336575868;T:422430316;N:30231989 51       404899388 344011831 336575868 422430316 30231989 SRX8790712 SRS7059104 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91044   0.09831   0.72801   0.47546   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60480 60480 SRR12287378 SRX8790711 SRS7059103 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1 GSM4681938   source name:36hpf zebrafish eyes|genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN overexpression|age:36hpf|tissue:eyes GSM4681938 GSM4681938: 36hpf zebrafish eyes; vsx2:Gal4>>Rab11aDN replicate 1; Danio rerio; RNA Seq GSM4681938   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681938 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_1.fq fastq 1642073673.0 32197523.0 GSM4681938 r1 0:51 A:429811686;C:368457771;G:362183885;T:449347598;N:32272733 51       429811686 368457771 362183885 449347598 32272733 SRX8790711 SRS7059103 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.90921   0.09675   0.73133   0.4816   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60481 60481 SRR12287377 SRX8790710 SRS7059102 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3 GSM4681937   source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN Control|age:36hpf|tissue:eyes GSM4681937 GSM4681937: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 3; Danio rerio; RNA Seq GSM4681937   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681937 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_Control_3.fq fastq 1580663604.0 30993404.0 GSM4681937 r1 0:51 A:412500071;C:356327817;G:348043781;T:432725076;N:31066859 51       412500071 356327817 348043781 432725076 31066859 SRX8790710 SRS7059102 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91358   0.09416   0.72756   0.47659   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60482 60482 SRR12287376 SRX8790709 SRS7059101 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2 GSM4681936   source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN Control|age:36hpf|tissue:eyes GSM4681936 GSM4681936: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 2; Danio rerio; RNA Seq GSM4681936   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681936 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_Control_2.fq fastq 1508085198.0 29570298.0 GSM4681936 r1 0:51 A:389591011;C:341465324;G:334342859;T:413045227;N:29640777 51       389591011 341465324 334342859 413045227 29640777 SRX8790709 SRS7059101 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91681   0.09096   0.72908   0.47951   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
60483 60483 SRR12287375 SRX8790708 SRS7059100 SRP273065 PRJNA647840 Rab11a recycling endosomes function to regulate cell signaling during retinal neurogenesis in zebrafish GSE154895 Transcriptome Analysis We report the transcriptional changes associated with inhibition of recycling endosome function within the developing zebrafish retina. Recycling endosome function was inhibited through transgenic expression of a Rab11a dominant negative protein within the developing retinal progenitor cells using UAS::mCherry Rab11aS25N; vsx2::Gal4 transgenic zebrafish. Changes in gene expression compared to vsx2:Gal4 controls were profiled through bulk RNA sequencing experiments of dissected zebrafish retinas. Gene expression changes resulting from inhibition of recycling endosome function were then compared to experiments in which canonical signaling pathways were modulated including activation of Notch signaling over expression of the constitutively active Notch1a intracellular domain; UAS::myc NICD1a; vsx2::Gal4 activation of Wnt signaling over expression of Wnt2b; UAS::EGFP Wnt2b;; vsx2::Gal4 activation of Hippo signaling over expression of nuclear retained YapS87A; dRED::UAS::YapS87A; vsx2::Gal4 and inhibition of mTor signaling through treatment of zebrafish embryos with Torrin. Overall design: 60 pooled eyes from experimental or control embryos were pooled for one sample. RNA sequencing experiments were performed in triplicate for each experimental condition.   pubmed:33634099   36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1 GSM4681935   source name:36hpf zebrafish eyes|genotype:Rab11aDN Control|age:36hpf|tissue:eyes 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1 Raw fastq files were aligned to Ensembl reference zv11 using STAR Aligned reads were cleaned using samtools Normalized read counts were obtained using HTSeq and edgeR Genome build: Danio Rerio Ensembl zv11 Supplementary files format and content: Counts per million normalized reads are available as a tab delimited file Normalized expression.txt and include YapS87A and WT samples from GSE71681 36hpf zebrafish eyes   Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads   genotype:Rab11aDN Control|age:36hpf|tissue:eyes GSM4681935 GSM4681935: 36hpf zebrafish eyes; Gal4 Control for Rab11aDN experiments; replicate 1; Danio rerio; RNA Seq GSM4681935   1 Dissected eyes were flash frozen on dry ice in pools of 60 per replicate. RNA was extracted using Trizol. polyA RNA; RNA libraries were prepared using standard Illumina protocols. Illumina HiSeq 2000; 50bp Single end reads GEO Accession:GSM4681935 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2000   SRP273065     Rab11aDN_Control_1.fq fastq 2010222018.0 39416118.0 GSM4681935 r1 0:51 A:517848834;C:456636261;G:445209526;T:551017897;N:39509500 51       517848834 456636261 445209526 551017897 39509500 SRX8790708 SRS7059100 SRA1102335 GEO Clark, Ophthalmology and Visual Sciences, Washington University 1 0.91683   0.09045   0.73105   0.4712   51   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk bulk bulk   United States 2020-07-22 Pharyngula Embryo Eye Sensory System
61585 61585 SRR12874658 SRX9340682 SRS7562491 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.   pubmed:30733552;pubmed:35034853   DR 32 hpf Rep5 [5 32 R] GSM4848081   source name:dorsal retina 32 hpf|hpf:32|tissue:dorsal retina DR 32 hpf Rep5 [5 32 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 32 hpf   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:32|tissue:dorsal retina GSM4848081 GSM4848081: DR 32 hpf Rep5 [5 32 R]; Danio rerio; RNA Seq GSM4848081   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:GSM4848081 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     5-32-R_R1.fastq.gz 5-32-R_R2.fastq.gz fastq fastq 3064655800.0 15323279.0 GSM4848081 r1 0:100 1:100 A:849671051;C:684088831;G:711976249;T:815743880;N:3175789 100 100     849671051 684088831 711976249 815743880 3175789 SRX9340682 SRS7562491 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.95057 0.9513 0.1194 0.11905 0.77494 0.77613 0.49604 0.49366 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61586 61586 SRR12874657 SRX9340681 SRS7562489 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.   pubmed:30733552;pubmed:35034853   OF 32 hpf Rep5 [5 32 0] GSM4848080   source name:optic fissure retina 32 hpf|hpf:32|tissue:optic fissure retina OF 32 hpf Rep5 [5 32 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 32 hpf   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:32|tissue:optic fissure retina GSM4848080 GSM4848080: OF 32 hpf Rep5 [5 32 0]; Danio rerio; RNA Seq GSM4848080   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:GSM4848080 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     5-32-O_R1.fastq.gz 5-32-O_R2.fastq.gz fastq fastq 2812293000.0 14061465.0 GSM4848080 r1 0:100 1:100 A:772408721;C:635228893;G:656655654;T:745205653;N:2794079 100 100     772408721 635228893 656655654 745205653 2794079 SRX9340681 SRS7562489 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.95042 0.94854 0.12201 0.12245 0.76656 0.76674 0.4902 0.45466 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61591 61591 SRR12874652 SRX9340676 SRS7562485 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.   pubmed:30733552;pubmed:35034853   DR 32 hpf Rep4 [4 32 R] GSM4848075   source name:dorsal retina 32 hpf|hpf:32|tissue:dorsal retina DR 32 hpf Rep4 [4 32 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 32 hpf   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:32|tissue:dorsal retina GSM4848075 GSM4848075: DR 32 hpf Rep4 [4 32 R]; Danio rerio; RNA Seq GSM4848075   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:GSM4848075 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     4-32-R_R1.fastq.gz 4-32-R_R2.fastq.gz fastq fastq 2568594800.0 12842974.0 GSM4848075 r1 0:100 1:100 A:714115878;C:571213430;G:592756757;T:687907919;N:2600816 100 100     714115878 571213430 592756757 687907919 2600816 SRX9340676 SRS7562485 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.94341 0.94276 0.13077 0.13061 0.77666 0.77786 0.50196 0.50235 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61592 61592 SRR12874651 SRX9340675 SRS7562483 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.   pubmed:30733552;pubmed:35034853   OF 32 hpf Rep4 [4 32 O] GSM4848074   source name:optic fissure retina 32 hpf|hpf:32|tissue:optic fissure retina OF 32 hpf Rep4 [4 32 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 32 hpf   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:32|tissue:optic fissure retina GSM4848074 GSM4848074: OF 32 hpf Rep4 [4 32 O]; Danio rerio; RNA Seq GSM4848074   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:GSM4848074 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     4-32-O_R1.fastq.gz 4-32-O_R2.fastq.gz fastq fastq 2862146800.0 14310734.0 GSM4848074 r1 0:100 1:100 A:798256994;C:632513285;G:657540252;T:770863343;N:2972926 100 100     798256994 632513285 657540252 770863343 2972926 SRX9340675 SRS7562483 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.94632 0.94555 0.12104 0.12143 0.76877 0.77153 0.50189 0.49752 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61597 61597 SRR12874646 SRX9340670 SRS7562479 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.   pubmed:30733552;pubmed:35034853   DR 32 hpf Rep3 [3 32 R] GSM4848069   source name:dorsal retina 32 hpf|hpf:32|tissue:dorsal retina DR 32 hpf Rep3 [3 32 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 32 hpf   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:32|tissue:dorsal retina GSM4848069 GSM4848069: DR 32 hpf Rep3 [3 32 R]; Danio rerio; RNA Seq GSM4848069   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:GSM4848069 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     3-32-R_R1.fastq.gz 3-32-R_R2.fastq.gz fastq fastq 2246467000.0 11232335.0 GSM4848069 r1 0:100 1:100 A:622134337;C:502407704;G:514466974;T:605332312;N:2125673 100 100     622134337 502407704 514466974 605332312 2125673 SRX9340670 SRS7562479 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.94802 0.94774 0.12772 0.12822 0.76319 0.76386 0.48432 0.48786 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61598 61598 SRR12874645 SRX9340669 SRS7562478 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.   pubmed:30733552;pubmed:35034853   OF 32 hpf Rep3 [3 32 O] GSM4848068   source name:optic fissure retina 32 hpf|hpf:32|tissue:optic fissure retina OF 32 hpf Rep3 [3 32 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 32 hpf   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:32|tissue:optic fissure retina GSM4848068 GSM4848068: OF 32 hpf Rep3 [3 32 O]; Danio rerio; RNA Seq GSM4848068   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:GSM4848068 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     3-32-O_R1.fastq.gz 3-32-O_R2.fastq.gz fastq fastq 2737545600.0 13687728.0 GSM4848068 r1 0:100 1:100 A:760551486;C:609584319;G:627992021;T:736550140;N:2867634 100 100     760551486 609584319 627992021 736550140 2867634 SRX9340669 SRS7562478 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.94605 0.94552 0.13901 0.13895 0.75649 0.75668 0.48125 0.48111 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61603 61603 SRR12874640 SRX9340664 SRS7562473 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.   pubmed:30733552;pubmed:35034853   DR 32 hpf Rep2 [2 32 R] GSM4848063   source name:dorsal retina 32 hpf|hpf:32|tissue:dorsal retina DR 32 hpf Rep2 [2 32 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 32 hpf   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:32|tissue:dorsal retina GSM4848063 GSM4848063: DR 32 hpf Rep2 [2 32 R]; Danio rerio; RNA Seq GSM4848063   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:GSM4848063 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     2-32-R_R1.fastq.gz 2-32-R_R2.fastq.gz fastq fastq 2547061600.0 12735308.0 GSM4848063 r1 0:100 1:100 A:704795519;C:569467305;G:590006212;T:680204159;N:2588405 100 100     704795519 569467305 590006212 680204159 2588405 SRX9340664 SRS7562473 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.94614 0.9465 0.1268 0.12657 0.77258 0.77287 0.45445 0.48314 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61604 61604 SRR12874639 SRX9340663 SRS7562472 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.   pubmed:30733552;pubmed:35034853   OF 32 hpf Rep2 [2 32 O] GSM4848062   source name:optic fissure retina 32 hpf|hpf:32|tissue:optic fissure retina OF 32 hpf Rep2 [2 32 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 32 hpf   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:32|tissue:optic fissure retina GSM4848062 GSM4848062: OF 32 hpf Rep2 [2 32 O]; Danio rerio; RNA Seq GSM4848062   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:GSM4848062 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     2-32-O_R1.fastq.gz 2-32-O_R2.fastq.gz fastq fastq 2693796000.0 13468980.0 GSM4848062 r1 0:100 1:100 A:755896770;C:592066498;G:614588530;T:728598306;N:2645896 100 100     755896770 592066498 614588530 728598306 2645896 SRX9340663 SRS7562472 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.9384 0.93872 0.14676 0.14702 0.77747 0.77796 0.50037 0.49799 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61609 61609 SRR12874634 SRX9340658 SRS7562468 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.   pubmed:30733552;pubmed:35034853   DR 32 hpf Rep1 [1 32 R] GSM4848057   source name:dorsal retina 32 hpf|hpf:32|tissue:dorsal retina DR 32 hpf Rep1 [1 32 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 32 hpf   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:32|tissue:dorsal retina GSM4848057 GSM4848057: DR 32 hpf Rep1 [1 32 R]; Danio rerio; RNA Seq GSM4848057   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:GSM4848057 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     1-32-R_R1.fastq.gz 1-32-R_R2.fastq.gz fastq fastq 1572192000.0 7860960.0 GSM4848057 r1 0:100 1:100 A:454955680;C:342136551;G:370912287;T:402534660;N:1652822 100 100     454955680 342136551 370912287 402534660 1652822 SRX9340658 SRS7562468 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.88484 0.88428 0.13525 0.13503 0.83 0.82972 0.4748 0.47499 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
61610 61610 SRR12874633 SRX9340657 SRS7562466 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.   pubmed:30733552;pubmed:35034853   OF 32 hpf Rep1 [1 32 O] GSM4848056   source name:optic fissure retina 32 hpf|hpf:32|tissue:optic fissure retina OF 32 hpf Rep1 [1 32 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 32 hpf   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:32|tissue:optic fissure retina GSM4848056 GSM4848056: OF 32 hpf Rep1 [1 32 O]; Danio rerio; RNA Seq GSM4848056   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:GSM4848056 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP288083     1-32-O_R1.fastq.gz 1-32-O_R2.fastq.gz fastq fastq 3392461400.0 16962307.0 GSM4848056 r1 0:100 1:100 A:969485728;C:748781124;G:792748695;T:878022482;N:3423371 100 100     969485728 748781124 792748695 878022482 3423371 SRX9340657 SRS7562466 SRA1146222 GEO Institute of Ophthalmology, UCL 2 0.83815 0.83039 0.14163 0.14041 0.8183 0.81929 0.53239 0.54149 100 100 B B biological fallback assumption illumina hiseq_era full_length cdna_unspecified smarter bulk unknown unknown   United Kingdom 2020-10-21 Pharyngula Embryo Eye Sensory System
68234 68234 SRR17691936 SRX13855153 SRS11731677 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Progenitors rep5 GSM5829847   tissue:Retina|age:42 hpf|expression of reporter genes:ath5 crx ptf1a Progenitors rep5 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5 crx ptf1a GSM5829847 GSM5829847: Progenitors rep5; Danio rerio; RNA Seq GSM5829847 r1 GSM5829847 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39847_Track-77463_R1.fastq.gz fastq 2671880168.0 35156318.0 GSM5829847 r1 0:76 A:758075890;C:556103961;G:567648726;T:789882254;N:169337 76       758075890 556103961 567648726 789882254 169337 SRX13855153 SRS11731677 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.86262   0.07481   0.82288   0.53123   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68235 68235 SRR17691937 SRX13855152 SRS11731678 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Amacrine cells/Horizontal cells rep5 GSM5829846   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ Amacrine cells/Horizontal cells rep5 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ GSM5829846 GSM5829846: Amacrine cells/Horizontal cells rep5; Danio rerio; RNA Seq GSM5829846 r1 GSM5829846 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39849_Track-77465_R1.fastq.gz fastq 2289732180.0 30128055.0 GSM5829846 r1 0:76 A:652374036;C:480127918;G:488180941;T:668911126;N:138159 76       652374036 480127918 488180941 668911126 138159 SRX13855152 SRS11731678 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.8739   0.08739   0.81292   0.52676   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68236 68236 SRR17691938 SRX13855151 SRS11731676 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Retinal ganglion cells rep5 GSM5829845   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a Retinal ganglion cells rep5 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a GSM5829845 GSM5829845: Retinal ganglion cells rep5; Danio rerio; RNA Seq GSM5829845 r1 GSM5829845 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39848_Track-77464_R1.fastq.gz fastq 2476332396.0 32583321.0 GSM5829845 r1 0:76 A:701512931;C:526534126;G:530739108;T:717386911;N:159320 76       701512931 526534126 530739108 717386911 159320 SRX13855151 SRS11731676 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.8617   0.08021   0.80996   0.51242   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68237 68237 SRR17691939 SRX13855150 SRS11731674 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Photoreceptors rep5 GSM5829844   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a Photoreceptors rep5 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a GSM5829844 GSM5829844: Photoreceptors rep5; Danio rerio; RNA Seq GSM5829844 r1 GSM5829844 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39846_Track-77462_R1.fastq.gz fastq 1616695940.0 21272315.0 GSM5829844 r1 0:76 A:464526547;C:335382772;G:339842014;T:476854782;N:89825 76       464526547 335382772 339842014 476854782 89825 SRX13855150 SRS11731674 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.86394   0.09242   0.8088   0.509   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68238 68238 SRR17691940 SRX13855149 SRS11731675 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Progenitors rep4 GSM5829843   tissue:Retina|age:42 hpf|expression of reporter genes:ath5 crx ptf1a Progenitors rep4 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5 crx ptf1a GSM5829843 GSM5829843: Progenitors rep4; Danio rerio; RNA Seq GSM5829843 r1 GSM5829843 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39843_Track-77459_R1.fastq.gz fastq 2082410640.0 27400140.0 GSM5829843 r1 0:76 A:585946840;C:444256500;G:450373929;T:601697561;N:135810 76       585946840 444256500 450373929 601697561 135810 SRX13855149 SRS11731675 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89577   0.06371   0.8294   0.50242   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68239 68239 SRR17691941 SRX13855148 SRS11731673 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Amacrine cells/Horizontal cells rep4 GSM5829842   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ Amacrine cells/Horizontal cells rep4 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ GSM5829842 GSM5829842: Amacrine cells/Horizontal cells rep4; Danio rerio; RNA Seq GSM5829842 r1 GSM5829842 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39845_Track-77461_R1.fastq.gz fastq 1892170404.0 24896979.0 GSM5829842 r1 0:76 A:531390170;C:407531534;G:410823674;T:542307947;N:117079 76       531390170 407531534 410823674 542307947 117079 SRX13855148 SRS11731673 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.87314   0.06249   0.82467   0.52118   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68240 68240 SRR17691942 SRX13855147 SRS11731672 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Retinal ganglion cells rep4 GSM5829841   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a Retinal ganglion cells rep4 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a GSM5829841 GSM5829841: Retinal ganglion cells rep4; Danio rerio; RNA Seq GSM5829841 r1 GSM5829841 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39844_Track-77460_R1.fastq.gz fastq 1987207416.0 26147466.0 GSM5829841 r1 0:76 A:554638061;C:429291877;G:433829568;T:569320821;N:127089 76       554638061 429291877 433829568 569320821 127089 SRX13855147 SRS11731672 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89782   0.05275   0.82148   0.45117   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68241 68241 SRR17691943 SRX13855146 SRS11731670 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Photoreceptors rep4 GSM5829840   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a Photoreceptors rep4 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a GSM5829840 GSM5829840: Photoreceptors rep4; Danio rerio; RNA Seq GSM5829840 r1 GSM5829840 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39842_Track-77458_R1.fastq.gz fastq 2489120536.0 32751586.0 GSM5829840 r1 0:76 A:704967195;C:528896131;G:534215449;T:720881738;N:160023 76       704967195 528896131 534215449 720881738 160023 SRX13855146 SRS11731670 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.8984   0.08364   0.79918   0.50877   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68242 68242 SRR17691944 SRX13855145 SRS11731671 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Progenitors rep3 GSM5829839   tissue:Retina|age:42 hpf|expression of reporter genes:ath5 crx ptf1a Progenitors rep3 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5 crx ptf1a GSM5829839 GSM5829839: Progenitors rep3; Danio rerio; RNA Seq GSM5829839 r1 GSM5829839 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39839_Track-77455_R1.fastq.gz fastq 2188476544.0 28795744.0 GSM5829839 r1 0:76 A:610646630;C:473306314;G:477638289;T:626748498;N:136813 76       610646630 473306314 477638289 626748498 136813 SRX13855145 SRS11731671 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.9028   0.0514   0.82276   0.51804   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68243 68243 SRR17691945 SRX13855144 SRS11731669 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Amacrine cells/Horizontal cells rep3 GSM5829838   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ Amacrine cells/Horizontal cells rep3 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ GSM5829838 GSM5829838: Amacrine cells/Horizontal cells rep3; Danio rerio; RNA Seq GSM5829838 r1 GSM5829838 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39841_Track-77457_R1.fastq.gz fastq 2248279500.0 29582625.0 GSM5829838 r1 0:76 A:634652526;C:474692656;G:482823598;T:655970424;N:140296 76       634652526 474692656 482823598 655970424 140296 SRX13855144 SRS11731669 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.85105   0.08121   0.84914   0.53121   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68244 68244 SRR17691946 SRX13855143 SRS11731668 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Retinal ganglion cells rep3 GSM5829837   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a Retinal ganglion cells rep3 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a GSM5829837 GSM5829837: Retinal ganglion cells rep3; Danio rerio; RNA Seq GSM5829837 r1 GSM5829837 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39840_Track-77456_R1.fastq.gz fastq 2220757544.0 29220494.0 GSM5829837 r1 0:76 A:626862785;C:473987199;G:479288977;T:640476226;N:142357 76       626862785 473987199 479288977 640476226 142357 SRX13855143 SRS11731668 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89921   0.07126   0.81077   0.51344   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68245 68245 SRR17691947 SRX13855142 SRS11731666 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Photoreceptors rep3 GSM5829836   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a Photoreceptors rep3 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a GSM5829836 GSM5829836: Photoreceptors rep3; Danio rerio; RNA Seq GSM5829836 r1 GSM5829836 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39838_Track-77454_R1.fastq.gz fastq 2200682524.0 28956349.0 GSM5829836 r1 0:76 A:628262884;C:463136167;G:467810265;T:641339201;N:134007 76       628262884 463136167 467810265 641339201 134007 SRX13855142 SRS11731666 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.90076   0.0794   0.80846   0.52313   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68246 68246 SRR17691948 SRX13855141 SRS11731667 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Progenitors rep2 GSM5829835   tissue:Retina|age:42 hpf|expression of reporter genes:ath5 crx ptf1a Progenitors rep2 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5 crx ptf1a GSM5829835 GSM5829835: Progenitors rep2; Danio rerio; RNA Seq GSM5829835 r1 GSM5829835 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39835_Track-77362_R1.fastq.gz fastq 2815769448.0 37049598.0 GSM5829835 r1 0:76 A:790349318;C:606022289;G:613105228;T:805997087;N:295526 76       790349318 606022289 613105228 805997087 295526 SRX13855141 SRS11731667 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.90321   0.06139   0.80892   0.51097   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68247 68247 SRR17691949 SRX13855140 SRS11731665 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Amacrine cells/Horizontal cells rep2 GSM5829834   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ Amacrine cells/Horizontal cells rep2 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ GSM5829834 GSM5829834: Amacrine cells/Horizontal cells rep2; Danio rerio; RNA Seq GSM5829834 r1 GSM5829834 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39837_Track-77453_R1.fastq.gz fastq 2809883020.0 36972145.0 GSM5829834 r1 0:76 A:807860837;C:580748384;G:590813546;T:830282953;N:177300 76       807860837 580748384 590813546 830282953 177300 SRX13855140 SRS11731665 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.85061   0.10745   0.82572   0.49992   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68248 68248 SRR17691950 SRX13855139 SRS11731663 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Retinal ganglion cells rep2 GSM5829833   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a Retinal ganglion cells rep2 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a GSM5829833 GSM5829833: Retinal ganglion cells rep2; Danio rerio; RNA Seq GSM5829833 r1 GSM5829833 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39836_Track-77363_R1.fastq.gz fastq 2592177296.0 34107596.0 GSM5829833 r1 0:76 A:737553116;C:547051858;G:554941945;T:752351979;N:278398 76       737553116 547051858 554941945 752351979 278398 SRX13855139 SRS11731663 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89081   0.07446   0.81919   0.5151   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68249 68249 SRR17691951 SRX13855138 SRS11731664 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Photoreceptors rep2 GSM5829832   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a Photoreceptors rep2 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a GSM5829832 GSM5829832: Photoreceptors rep2; Danio rerio; RNA Seq GSM5829832 r1 GSM5829832 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39834_Track-77361_R1.fastq.gz fastq 2635963632.0 34683732.0 GSM5829832 r1 0:76 A:750601681;C:559002807;G:566038765;T:760044927;N:275452 76       750601681 559002807 566038765 760044927 275452 SRX13855138 SRS11731664 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.90002   0.06852   0.81568   0.47671   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68250 68250 SRR17691952 SRX13855137 SRS11731662 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Progenitors rep1 GSM5829831   tissue:Retina|age:42 hpf|expression of reporter genes:ath5 crx ptf1a Progenitors rep1 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5 crx ptf1a GSM5829831 GSM5829831: Progenitors rep1; Danio rerio; RNA Seq GSM5829831 r1 GSM5829831 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39832_Track-77359_R1.fastq.gz fastq 2184577820.0 28744445.0 GSM5829831 r1 0:76 A:627633686;C:452127477;G:463833090;T:640750578;N:232989 76       627633686 452127477 463833090 640750578 232989 SRX13855137 SRS11731662 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89216   0.07417   0.80225   0.52375   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68251 68251 SRR17691953 SRX13855136 SRS11731661 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Amacrine cells/Horizontal cells rep1 GSM5829830   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ Amacrine cells/Horizontal cells rep1 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a+ GSM5829830 GSM5829830: Amacrine cells/Horizontal cells rep1; Danio rerio; RNA Seq GSM5829830 r1 GSM5829830 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39830_Track-77357_R1.fastq.gz fastq 3109563332.0 40915307.0 GSM5829830 r1 0:76 A:899644244;C:633901122;G:650143611;T:925537182;N:337173 76       899644244 633901122 650143611 925537182 337173 SRX13855136 SRS11731661 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.85494   0.11905   0.87667   0.5511   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68252 68252 SRR17691954 SRX13855135 SRS11731660 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Retinal ganglion cells rep1 GSM5829829   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx ptf1a Retinal ganglion cells rep1 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx ptf1a GSM5829829 GSM5829829: Retinal ganglion cells rep1; Danio rerio; RNA Seq GSM5829829 r1 GSM5829829 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39831_Track-77358_R1.fastq.gz fastq 2488702308.0 32746083.0 GSM5829829 r1 0:76 A:707088697;C:530173993;G:534760661;T:716411428;N:267529 76       707088697 530173993 534760661 716411428 267529 SRX13855135 SRS11731660 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.89004   0.07677   0.80984   0.50365   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System
68253 68253 SRR17691955 SRX13855134 SRS11731659 SRP356155 PRJNA799333 RNA seq dataset of different neuronal cell types and progenitors in the developing zebrafish retina at 42 hpf GSE194158 Transcriptome Analysis This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hpf: retinal ganglion cells photoreceptors inhibitory neurons amacrine cells and horizontal cells and progenitor cells. Overall design: Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled.       Photoreceptors rep1 GSM5829828   tissue:Retina|age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a Photoreceptors rep1 Basecalling performed using bcl2fastq version 2.19.1 Read alignment performed using GSNAP version 2018 07 04 gsnap d GRCz11 gunzip A sam t 6 use sarray=1 input buffer size=500000 output buffer size=500000 B 5 N 0 n 1 s EnsemblGene 95.ss.GRCz11.iit read group platform=illumina  Read counting performed using featureCounts version 1.6.3  featureCounts a annotation/danio rerio/GRCz11/EnsemblGene 95.GRCz11.TR.gtf s 0 Q 1 T 8 Genome build: Danio rerio GRCz10 Supplementary files format and content: Matrix table .xlsx with normalised gene counts for every gene and every sample Supplementary files format and content: Matrix table .txt with raw gene counts for every gene and every sample Retina MS 222 0.01% prior to dissection of the retinas. Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads. Embryos were incubated at 28ºC until 24 hpf then at 21ºC until 30 hpf and finally at 28ºC until 42 hpf. age:42 hpf|expression of reporter genes:ath5+ crx+ ptf1a GSM5829828 GSM5829828: Photoreceptors rep1; Danio rerio; RNA Seq GSM5829828 r1 GSM5829828 1 Retinal cell types were sorted from dissociated zebrafish retinas at 42 hpf using the triple transgenic line Tgath5:gap RFP Tgcrx:gap CFP Tgptf1a:gal4 UAS:gap YFP. For each of the 5 replicates 25 retinas were pooled. During dissection retinas were maintained at 4°C in a volume of 100 µl in PBS. Prior to dissociation the volume was adjusted to 500 µl. Manual dissociation was performed immediately before FACS using BSA coated glass pipettes. 500 cells per sample were FACS sorted directly into extraction buffer. Superscript II was used for reverse transcription and cDNA was amplified using Kapa HiFi HotStart Readymix Peqlab. Purification of the amplified cDNA was performed using Ampure XP Beads Beckman Coulter. Libraries were prepared accoridng to SmartSeq 2 flex Illumina protocol. Illumina sequencing was performed on a Nextseq500 with a sample sequencing depth of at least 30 mio reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP356155   loader:fastq load.py L39833_Track-77360_R1.fastq.gz fastq 1992015632.0 26210732.0 GSM5829828 r1 0:76 A:567270537;C:418033884;G:425507861;T:580998753;N:204597 76       567270537 418033884 425507861 580998753 204597 SRX13855134 SRS11731659 SRA1360146 Max Planck Institute of Molecular Cell Biology and Genetics Max Planck Institute of Molecular Cell Biology and Genetics 1 0.88374   0.06752   0.82731   0.54807   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   Germany 2022-01-21 Pharyngula Embryo Eye Sensory System

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