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1,223 rows where devstage_curation = "Hatching" and technology = "smartseq"

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tissue_curation 6

experiment.library_selection 3

experiment.library_layout 2

technology 1

  • smartseq · 1,223 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Hatching · 1,223 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
19087 19087 ERR13834862 ERX13237628 ERS21098715 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC1 S20 R1 001.fastq.gz SAMEA116100635 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC1|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC1|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC1 webin reads 48 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC1_S20_R1_001.fastq.gz fastq 3768442091.0 38065677.0 webin reads 48 HC1 0:99.00 A:1055463738;C:792073627;G:817607736;T:1103223790;N:73200 99       1055463738 792073627 817607736 1103223790 73200 ERX13237628 ERS21098715 ERA30883416 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19088 19088 ERR13834951 ERX13237717 ERS21098721 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR3 S26 R1 001.fastq.gz 58 PR3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR3 webin reads 58 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR3_S26_R1_001.fastq.gz fastq 3869469736.0 38850717.0 webin reads 58 PR3 0:99.60 A:1103909449;C:804146524;G:827344036;T:1134036010;N:33717 99       1103909449 804146524 827344036 1134036010 33717 ERX13237717 ERS21098721 ERA30883529 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19089 19089 ERR13835010 ERX13237776 ERS21098726 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC4 S31 R1 001.fastq.gz SAMEA116100646 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 AC4|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 AC4|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 AC4 webin reads 58 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC4_S31_R1_001.fastq.gz fastq 3607648651.0 36331933.0 webin reads 58 AC4 0:99.30 A:1038047870;C:736262498;G:759315202;T:1073962987;N:60094 99       1038047870 736262498 759315202 1073962987 60094 ERX13237776 ERS21098726 ERA30883721 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19090 19090 ERR13822794 ERX13225546 ERS21098708 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR2 S13 R1 001.fastq.gz 48 PR2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR2 webin reads 48 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR2_S13_R1_001.fastq.gz fastq 3809299607.0 38404185.0 webin reads 48 PR2 0:99.19 A:1067728192;C:802585802;G:828435932;T:1110435904;N:113777 99       1067728192 802585802 828435932 1110435904 113777 ERX13225546 ERS21098708 ERA30879682 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19091 19091 ERR13834854 ERX13237620 ERS21098714 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC4 S19 R1 001.fastq.gz 48 AC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC4 webin reads 48 AC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC4_S19_R1_001.fastq.gz fastq 3410801894.0 34443068.0 webin reads 48 AC4 0:99.03 A:966160063;C:707754156;G:733039262;T:1003772756;N:75657 99       966160063 707754156 733039262 1003772756 75657 ERX13237620 ERS21098714 ERA30883390 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19092 19092 ERR13828824 ERX13231590 ERS21098710 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR4 S15 R1 001.fastq.gz 48 PR4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR4 webin reads 48 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR4_S15_R1_001.fastq.gz fastq 4365943927.0 44278278.0 webin reads 48 PR4 0:98.60 A:1214448497;C:927512154;G:957491418;T:1266385355;N:106503 98       1214448497 927512154 957491418 1266385355 106503 ERX13231590 ERS21098710 ERA30883309 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19093 19093 ERR13834993 ERX13237759 ERS21098723 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC1 S28 R1 001.fastq.gz 58 AC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC1 webin reads 58 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC1_S28_R1_001.fastq.gz fastq 3710768269.0 37364763.0 webin reads 58 AC1 0:99.31 A:1060419097;C:761984557;G:786533722;T:1101603428;N:227465 99       1060419097 761984557 786533722 1101603428 227465 ERX13237759 ERS21098723 ERA30883659 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19094 19094 ERR13834875 ERX13237641 ERS21098717 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC3 S22 R1 001.fastq.gz 48 HC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC3 webin reads 48 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC3_S22_R1_001.fastq.gz fastq 3083078586.0 31073491.0 webin reads 48 HC3 0:99.22 A:856250957;C:655140994;G:677078911;T:894558582;N:49142 99       856250957 655140994 677078911 894558582 49142 ERX13237641 ERS21098717 ERA30883447 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19095 19095 ERR13834899 ERX13237665 ERS21098720 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR2 S25 R1 001.fastq.gz 58 PR2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR2 webin reads 58 PR2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR2_S25_R1_001.fastq.gz fastq 3849571818.0 38706841.0 webin reads 58 PR2 0:99.45 A:1089593011;C:803322469;G:827777017;T:1128836774;N:42547 99       1089593011 803322469 827777017 1128836774 42547 ERX13237665 ERS21098720 ERA30883518 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19096 19096 ERR13834889 ERX13237655 ERS21098719 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR1 S24 R1 001.fastq.gz 58 PR1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR1 webin reads 58 PR1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR1_S24_R1_001.fastq.gz fastq 3945671240.0 39514922.0 webin reads 58 PR1 0:99.85 A:1135075173;C:807489123;G:827964380;T:1175109762;N:32802 99       1135075173 807489123 827964380 1175109762 32802 ERX13237655 ERS21098719 ERA30883497 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19097 19097 ERR13835019 ERX13237785 ERS21098728 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC2 S33 R1 001.fastq.gz SAMEA116100648 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:58 HC2|collected by:Jaakko Lehtimaki|collection date:2021 12 02|common name:zebrafish|dev stage:58 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:58 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 58 HC2 webin reads 58 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC2_S33_R1_001.fastq.gz fastq 3711237069.0 37217240.0 webin reads 58 HC2 0:99.72 A:1070592288;C:757099665;G:780689044;T:1102575310;N:280762 99       1070592288 757099665 780689044 1102575310 280762 ERX13237785 ERS21098728 ERA30883748 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19100 19100 ERR13828836 ERX13231602 ERS21098712 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC2 S17 R1 001.fastq.gz 48 AC2   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC2 webin reads 48 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC2_S17_R1_001.fastq.gz fastq 3205206588.0 32424632.0 webin reads 48 AC2 0:98.85 A:902438127;C:672433401;G:694813369;T:935445436;N:76255 98       902438127 672433401 694813369 935445436 76255 ERX13231602 ERS21098712 ERA30883343 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19101 19101 ERR13835004 ERX13237770 ERS21098725 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC3 S30 R1 001.fastq.gz 58 AC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC3 webin reads 58 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC3_S30_R1_001.fastq.gz fastq 3782993133.0 38295959.0 webin reads 58 AC3 0:98.78 A:1080745150;C:779903026;G:803258485;T:1118994941;N:91531 98       1080745150 779903026 803258485 1118994941 91531 ERX13237770 ERS21098725 ERA30883697 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19102 19102 ERR13834868 ERX13237634 ERS21098716 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC2 S21 R1 001.fastq.gz SAMEA116100636 GIMM ENA first public:2024 01 01|INSDC center name:GIMM|INSDC status:public|Submitter Id:48 HC2|collected by:Jaakko Lehtimaki|collection date:2021 11 24|common name:zebrafish|dev stage:48 hpf location country and/or sea:Portugal|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|sample name:48 HC2|scientific name:Danio rerio|tissue type:retina                 Raw reads: 48 HC2 webin reads 48 HC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC2_S21_R1_001.fastq.gz fastq 3424347865.0 34510204.0 webin reads 48 HC2 0:99.23 A:959488173;C:721171249;G:745705870;T:997922014;N:60559 99       959488173 721171249 745705870 997922014 60559 ERX13237634 ERS21098716 ERA30883434 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2024-01-01 Hatching Embryo Eye Sensory System
19104 19104 ERR13834880 ERX13237646 ERS21098718 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48HC4 S23 R1 001.fastq.gz 48 HC4   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 HC4 webin reads 48 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48HC4_S23_R1_001.fastq.gz fastq 3660674315.0 36821474.0 webin reads 48 HC4 0:99.42 A:1035049987;C:763030378;G:788062167;T:1074303516;N:228267 99       1035049987 763030378 788062167 1074303516 228267 ERX13237646 ERS21098718 ERA30883470 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19105 19105 ERR13822867 ERX13225633 ERS21098709 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48PR3 S14 R1 001.fastq.gz 48 PR3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 PR3 webin reads 48 PR3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 PR3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48PR3_S14_R1_001.fastq.gz fastq 4232170464.0 42534853.0 webin reads 48 PR3 0:99.50 A:1195251409;C:889346003;G:917240118;T:1230272855;N:60079 99       1195251409 889346003 917240118 1230272855 60079 ERX13225633 ERS21098709 ERA30879704 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19108 19108 ERR13828843 ERX13234350 ERS21098713 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC3 S18 R1 001.fastq.gz 48 AC3   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC3 webin reads 48 AC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC3_S18_R1_001.fastq.gz fastq 3733628911.0 37779462.0 webin reads 48 AC3 0:98.83 A:1047204450;C:786943605;G:812327274;T:1086893109;N:260473 98       1047204450 786943605 812327274 1086893109 260473 ERX13234350 ERS21098713 ERA30883366 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19113 19113 ERR13835032 ERX13237798 ERS21098730 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC4 S35 R1 001.fastq.gz 58 HC4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC4 webin reads 58 HC4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC4_S35_R1_001.fastq.gz fastq 4418556015.0 44331835.0 webin reads 58 HC4 0:99.67 A:1255080581;C:916490847;G:946212615;T:1300735054;N:36918 99       1255080581 916490847 946212615 1300735054 36918 ERX13237798 ERS21098730 ERA30883773 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19114 19114 ERR13828829 ERX13231595 ERS21098711 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 48AC1 S16 R1 001.fastq.gz 48 AC1   organism:Danio rerio|collection date:2021 11 24|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:48 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 48 AC1 webin reads 48 AC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 48 AC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 48AC1_S16_R1_001.fastq.gz fastq 3933669121.0 39695406.0 webin reads 48 AC1 0:99.10 A:1105258159;C:824538054;G:854253688;T:1149538152;N:81068 99       1105258159 824538054 854253688 1149538152 81068 ERX13231595 ERS21098711 ERA30883326 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19117 19117 ERR13835025 ERX13237791 ERS21098729 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC3 S34 R1 001.fastq.gz 58 HC3   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC3 webin reads 58 HC3         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC3 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC3_S34_R1_001.fastq.gz fastq 3523899212.0 35292613.0 webin reads 58 HC3 0:99.85 A:1012516999;C:723225071;G:745152410;T:1042976092;N:28640 99       1012516999 723225071 745152410 1042976092 28640 ERX13237791 ERS21098729 ERA30883757 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19118 19118 ERR13835014 ERX13237780 ERS21098727 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58HC1 S32 R1 001.fastq.gz 58 HC1   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 HC1 webin reads 58 HC1         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 HC1 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58HC1_S32_R1_001.fastq.gz fastq 3436493821.0 34597887.0 webin reads 58 HC1 0:99.33 A:980894291;C:707196785;G:729948858;T:1018400124;N:53763 99       980894291 707196785 729948858 1018400124 53763 ERX13237780 ERS21098727 ERA30883731 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19119 19119 ERR13834987 ERX13237753 ERS21098722 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58PR4 S27 R1 001.fastq.gz 58 PR4   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 PR4 webin reads 58 PR4         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 PR4 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58PR4_S27_R1_001.fastq.gz fastq 3069040814.0 30923422.0 webin reads 58 PR4 0:99.25 A:875776938;C:633951750;G:653308475;T:905949639;N:54012 99       875776938 633951750 653308475 905949639 54012 ERX13237753 ERS21098722 ERA30883641 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
19121 19121 ERR13834997 ERX13237763 ERS21098724 ERP164534 PRJEB80557 RNAseq of Danio Rerio Photoreceptors Amacrine and Horizontal cells collected 38 48 and 58 hpf e09e99a9-eabd-4a7d-8f92-2c4cf9f384ed Other This analysis was conducted to elucidate potential guidance of retinal horizontal cells HCs by photoreceptors PRs and/or amacrine cells ACs during the retinal lamination. We dissected retinae from three different developmental stages corresponding to different stages in HCs lamination process and separated HCs PRs and HCs based on their differential GFP and DsRed expression in the Lhx1:GFP; ptf1a:DsRed zebrafish transgenic line. Four replicates of each sample were lysed converted to cDNA sequenced using the SMART SEQ2 protocol. ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01   retinal neurons 58AC2 S29 R1 001.fastq.gz 58 AC2   organism:Danio rerio|collection date:2021 12 02|scientific name:Danio rerio|collected by:Jaakko Lehtimaki|common name:zebrafish|lab host:Tg 5.5ptf1a:DsRed; Tglhx1a:EGFP|dev stage:58 hpf type:retina|geographic location country and/or sea:Portugal                 Raw reads: 58 AC2 webin reads 58 AC2         RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq X   ERP164534 Raw reads: 58 AC2 ENA FIRST PUBLIC:2025 01 01|ENA LAST UPDATE:2025 01 01 58AC2_S29_R1_001.fastq.gz fastq 3872162091.0 38898173.0 webin reads 58 AC2 0:99.55 A:1111663794;C:793747086;G:817730996;T:1148980297;N:39918 99       1111663794 793747086 817730996 1148980297 39918 ERX13237763 ERS21098724 ERA30883678 Gulbenkian Institute for Molecular Medicine|European Nucleotide Archive Gulbenkian Institute for Molecular Medicine                       B   usable mapping rate illumina hiseq_era unknown random_priming unknown sc single_cell_plate smartseq   Belgium 2025-01-01 Hatching Embryo Eye Sensory System
29909 29909 SRR27592934 SRX23261746 SRS20163710 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep11 GSM8020192   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020192 GSM8020192: deaf1 2 dpf rep11; Danio rerio; RNA Seq GSM8020192 r1 GSM8020192 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D28_S56_R1_001.fastq.gz fastq 4475806200.0 44758062.0 GSM8020192 r1 0:100 A:1106171674;C:1156870042;G:1092472583;T:1120212338;N:79563 100       1106171674 1156870042 1092472583 1120212338 79563 SRX23261746 SRS20163710 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29910 29910 SRR27592935 SRX23261745 SRS20163711 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep10 GSM8020191   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020191 GSM8020191: deaf1 2 dpf rep10; Danio rerio; RNA Seq GSM8020191 r1 GSM8020191 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D27_S55_R1_001.fastq.gz fastq 4001586700.0 40015867.0 GSM8020191 r1 0:100 A:1000059012;C:1020300240;G:981249122;T:999909425;N:68901 100       1000059012 1020300240 981249122 999909425 68901 SRX23261745 SRS20163711 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29911 29911 SRR27592936 SRX23261744 SRS20163709 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep9 GSM8020190   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020190 GSM8020190: deaf1 2 dpf rep9; Danio rerio; RNA Seq GSM8020190 r1 GSM8020190 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D26_S54_R1_001.fastq.gz fastq 3716740300.0 37167403.0 GSM8020190 r1 0:100 A:930732486;C:940157658;G:908687307;T:937097122;N:65727 100       930732486 940157658 908687307 937097122 65727 SRX23261744 SRS20163709 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29912 29912 SRR27592937 SRX23261743 SRS20163708 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep8 GSM8020189   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020189 GSM8020189: deaf1 2 dpf rep8; Danio rerio; RNA Seq GSM8020189 r1 GSM8020189 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D25_S53_R1_001.fastq.gz fastq 3741485000.0 37414850.0 GSM8020189 r1 0:100 A:929440558;C:958986044;G:914039968;T:938952561;N:65869 100       929440558 958986044 914039968 938952561 65869 SRX23261743 SRS20163708 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29913 29913 SRR27592938 SRX23261742 SRS20163707 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep7 GSM8020188   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020188 GSM8020188: deaf1 2 dpf rep7; Danio rerio; RNA Seq GSM8020188 r1 GSM8020188 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D24_S52_R1_001.fastq.gz fastq 2971991400.0 29719914.0 GSM8020188 r1 0:100 A:738636815;C:755836125;G:729168292;T:748297854;N:52314 100       738636815 755836125 729168292 748297854 52314 SRX23261742 SRS20163707 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29914 29914 SRR27592939 SRX23261741 SRS20163706 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep6 GSM8020187   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020187 GSM8020187: deaf1 2 dpf rep6; Danio rerio; RNA Seq GSM8020187 r1 GSM8020187 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D23_S51_R1_001.fastq.gz fastq 4134397800.0 41343978.0 GSM8020187 r1 0:100 A:1032735373;C:1051188374;G:1016197596;T:1034203095;N:73362 100       1032735373 1051188374 1016197596 1034203095 73362 SRX23261741 SRS20163706 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29915 29915 SRR27592940 SRX23261740 SRS20163705 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep5 GSM8020186   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020186 GSM8020186: deaf1 2 dpf rep5; Danio rerio; RNA Seq GSM8020186 r1 GSM8020186 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D22_S50_R1_001.fastq.gz fastq 3631624500.0 36316245.0 GSM8020186 r1 0:100 A:901094303;C:929956244;G:893844528;T:906664233;N:65192 100       901094303 929956244 893844528 906664233 65192 SRX23261740 SRS20163705 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29916 29916 SRR27592941 SRX23261739 SRS20163704 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep4 GSM8020185   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i homozygous GSM8020185 GSM8020185: deaf1 2 dpf rep4; Danio rerio; RNA Seq GSM8020185 r1 GSM8020185 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-hom_D21_S49_R1_001.fastq.gz fastq 3349609200.0 33496092.0 GSM8020185 r1 0:100 A:835857971;C:854981364;G:824035698;T:834673793;N:60374 100       835857971 854981364 824035698 834673793 60374 SRX23261739 SRS20163704 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29917 29917 SRR27592942 SRX23261738 SRS20163703 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep3 GSM8020184   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020184 GSM8020184: deaf1 2 dpf rep3; Danio rerio; RNA Seq GSM8020184 r1 GSM8020184 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D20_S48_R1_001.fastq.gz fastq 3371713300.0 33717133.0 GSM8020184 r1 0:100 A:839050016;C:857965663;G:828869795;T:845766740;N:61086 100       839050016 857965663 828869795 845766740 61086 SRX23261738 SRS20163703 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29918 29918 SRR27592943 SRX23261737 SRS20163701 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep2 GSM8020183   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020183 GSM8020183: deaf1 2 dpf rep2; Danio rerio; RNA Seq GSM8020183 r1 GSM8020183 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D18_S46_R1_001.fastq.gz fastq 3756501100.0 37565011.0 GSM8020183 r1 0:100 A:938612608;C:949004833;G:927692516;T:941125085;N:66058 100       938612608 949004833 927692516 941125085 66058 SRX23261737 SRS20163701 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29919 29919 SRR27592944 SRX23261736 SRS20163702 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep1 GSM8020182   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous|geo loc name:missing|collection date:missing deaf1 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i heterozygous GSM8020182 GSM8020182: deaf1 2 dpf rep1; Danio rerio; RNA Seq GSM8020182 r1 GSM8020182 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-het_D17_S45_R1_001.fastq.gz fastq 3378074100.0 33780741.0 GSM8020182 r1 0:100 A:839320911;C:859028175;G:836373251;T:843291522;N:60241 100       839320911 859028175 836373251 843291522 60241 SRX23261736 SRS20163702 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29920 29920 SRR27592945 SRX23261735 SRS20163699 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep13 GSM8020181   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020181 GSM8020181: deaf1 t238p 2 dpf rep13; Danio rerio; RNA Seq GSM8020181 r1 GSM8020181 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST4.fastq.gz fastq 2522881653.0 33818740.0 GSM8020181 r1 0:74.60 A:655207900;C:616856238;G:613068980;T:637525231;N:223304 74       655207900 616856238 613068980 637525231 223304 SRX23261735 SRS20163699 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29921 29921 SRR27592946 SRX23261734 SRS20163698 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep12 GSM8020180   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020180 GSM8020180: deaf1 t238p 2 dpf rep12; Danio rerio; RNA Seq GSM8020180 r1 GSM8020180 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST3.fastq.gz fastq 3232696302.0 43332777.0 GSM8020180 r1 0:74.60 A:838706781;C:792017578;G:780975426;T:820709157;N:287360 74       838706781 792017578 780975426 820709157 287360 SRX23261734 SRS20163698 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29922 29922 SRR27592947 SRX23261733 SRS20163700 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep11 GSM8020179   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020179 GSM8020179: deaf1 t238p 2 dpf rep11; Danio rerio; RNA Seq GSM8020179 r1 GSM8020179 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST2.fastq.gz fastq 3105671470.0 41634840.0 GSM8020179 r1 0:74.59 A:797054679;C:770109006;G:759275000;T:778955169;N:277616 74       797054679 770109006 759275000 778955169 277616 SRX23261733 SRS20163700 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29923 29923 SRR27592948 SRX23261732 SRS20163697 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep10 GSM8020178   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p wild types GSM8020178 GSM8020178: deaf1 t238p 2 dpf rep10; Danio rerio; RNA Seq GSM8020178 r1 GSM8020178 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-wt_ST1.fastq.gz fastq 3499217864.0 46905154.0 GSM8020178 r1 0:74.60 A:893360259;C:869418642;G:860403580;T:875711902;N:323481 74       893360259 869418642 860403580 875711902 323481 SRX23261732 SRS20163697 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29924 29924 SRR27592949 SRX23261731 SRS20163696 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep9 GSM8020177   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020177 GSM8020177: deaf1 t238p 2 dpf rep9; Danio rerio; RNA Seq GSM8020177 r1 GSM8020177 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST8.fastq.gz fastq 3268771798.0 43820118.0 GSM8020177 r1 0:74.60 A:847366551;C:800849702;G:791226044;T:829037606;N:291895 74       847366551 800849702 791226044 829037606 291895 SRX23261731 SRS20163696 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29925 29925 SRR27592950 SRX23261730 SRS20163695 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep8 GSM8020176   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020176 GSM8020176: deaf1 t238p 2 dpf rep8; Danio rerio; RNA Seq GSM8020176 r1 GSM8020176 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST7.fastq.gz fastq 2027174325.0 27178466.0 GSM8020176 r1 0:74.59 A:525317640;C:498055852;G:491357881;T:512263813;N:179139 74       525317640 498055852 491357881 512263813 179139 SRX23261730 SRS20163695 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29926 29926 SRR27592951 SRX23261729 SRS20163694 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep7 GSM8020175   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020175 GSM8020175: deaf1 t238p 2 dpf rep7; Danio rerio; RNA Seq GSM8020175 r1 GSM8020175 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST6.fastq.gz fastq 2787340348.0 37363599.0 GSM8020175 r1 0:74.60 A:722896986;C:681138747;G:674833627;T:708219281;N:251707 74       722896986 681138747 674833627 708219281 251707 SRX23261729 SRS20163694 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29927 29927 SRR27592952 SRX23261728 SRS20163693 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep6 GSM8020174   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p homozygous GSM8020174 GSM8020174: deaf1 t238p 2 dpf rep6; Danio rerio; RNA Seq GSM8020174 r1 GSM8020174 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-hom_ST5.fastq.gz fastq 2977171544.0 39908640.0 GSM8020174 r1 0:74.60 A:770250088;C:731344480;G:721594408;T:753713587;N:268981 74       770250088 731344480 721594408 753713587 268981 SRX23261728 SRS20163693 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29928 29928 SRR27592953 SRX23261727 SRS20163692 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep5 GSM8020173   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020173 GSM8020173: deaf1 t238p 2 dpf rep5; Danio rerio; RNA Seq GSM8020173 r1 GSM8020173 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST9.fastq.gz fastq 2546529762.0 34141024.0 GSM8020173 r1 0:74.59 A:665391714;C:618921995;G:614059292;T:647931593;N:225168 74       665391714 618921995 614059292 647931593 225168 SRX23261727 SRS20163692 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29929 29929 SRR27592954 SRX23261726 SRS20163691 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep4 GSM8020172   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020172 GSM8020172: deaf1 t238p 2 dpf rep4; Danio rerio; RNA Seq GSM8020172 r1 GSM8020172 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST13.fastq.gz fastq 3176861738.0 42588753.0 GSM8020172 r1 0:74.59 A:831927955;C:768758728;G:763547713;T:812339162;N:288180 74       831927955 768758728 763547713 812339162 288180 SRX23261726 SRS20163691 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29930 29930 SRR27592955 SRX23261725 SRS20163690 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep3 GSM8020171   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020171 GSM8020171: deaf1 t238p 2 dpf rep3; Danio rerio; RNA Seq GSM8020171 r1 GSM8020171 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST12.fastq.gz fastq 1136232560.0 15234548.0 GSM8020171 r1 0:74.58 A:297385645;C:276022399;G:273402666;T:289320311;N:101539 74       297385645 276022399 273402666 289320311 101539 SRX23261725 SRS20163690 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29931 29931 SRR27592956 SRX23261724 SRS20163689 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep2 GSM8020170   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020170 GSM8020170: deaf1 t238p 2 dpf rep2; Danio rerio; RNA Seq GSM8020170 r1 GSM8020170 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST11.fastq.gz fastq 2735749019.0 36680185.0 GSM8020170 r1 0:74.58 A:721197113;C:659588175;G:652875625;T:701848626;N:239480 74       721197113 659588175 652875625 701848626 239480 SRX23261724 SRS20163689 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29932 29932 SRR27592957 SRX23261723 SRS20163688 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 t238p 2 dpf rep1 GSM8020169   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous|geo loc name:missing|collection date:missing deaf1 t238p 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 t238p heterozygous GSM8020169 GSM8020169: deaf1 t238p 2 dpf rep1; Danio rerio; RNA Seq GSM8020169 r1 GSM8020169 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 550   SRP484215     deaf1-t238p-2dpf-het_ST10.fastq.gz fastq 3369699901.0 45178398.0 GSM8020169 r1 0:74.59 A:883991145;C:814741172;G:809532162;T:861133903;N:301519 74       883991145 814741172 809532162 861133903 301519 SRX23261723 SRS20163688 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina nextseq unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29947 29947 SRR27592972 SRX23261708 SRS20163673 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep13 GSM8020168   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020168 GSM8020168: deaf1 c207y 2 dpf rep13; Danio rerio; RNA Seq GSM8020168 r1 GSM8020168 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_B2_S14_R1_001.fastq.gz fastq 2963811367.0 29344667.0 GSM8020168 r1 0:101 A:803333990;C:685431342;G:677569210;T:797384558;N:92267 101       803333990 685431342 677569210 797384558 92267 SRX23261708 SRS20163673 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29948 29948 SRR27592973 SRX23261707 SRS20163672 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep12 GSM8020167   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020167 GSM8020167: deaf1 c207y 2 dpf rep12; Danio rerio; RNA Seq GSM8020167 r1 GSM8020167 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_B1_S13_R1_001.fastq.gz fastq 3184165289.0 31526389.0 GSM8020167 r1 0:101 A:847208990;C:751109498;G:736855605;T:848892893;N:98303 101       847208990 751109498 736855605 848892893 98303 SRX23261707 SRS20163672 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29949 29949 SRR27592974 SRX23261706 SRS20163671 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep11 GSM8020166   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep11 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020166 GSM8020166: deaf1 c207y 2 dpf rep11; Danio rerio; RNA Seq GSM8020166 r1 GSM8020166 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A12_S12_R1_001.fastq.gz fastq 3115838183.0 30849883.0 GSM8020166 r1 0:101 A:846133299;C:724401184;G:709966835;T:835240904;N:95961 101       846133299 724401184 709966835 835240904 95961 SRX23261706 SRS20163671 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29950 29950 SRR27592975 SRX23261705 SRS20163670 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep10 GSM8020165   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep10 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020165 GSM8020165: deaf1 c207y 2 dpf rep10; Danio rerio; RNA Seq GSM8020165 r1 GSM8020165 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A11_S11_R1_001.fastq.gz fastq 2767984184.0 27405784.0 GSM8020165 r1 0:101 A:753665483;C:638171516;G:626255827;T:749805524;N:85834 101       753665483 638171516 626255827 749805524 85834 SRX23261705 SRS20163670 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29951 29951 SRR27592976 SRX23261704 SRS20163669 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep9 GSM8020164   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep9 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y wild types GSM8020164 GSM8020164: deaf1 c207y 2 dpf rep9; Danio rerio; RNA Seq GSM8020164 r1 GSM8020164 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-wt_A10_S10_R1_001.fastq.gz fastq 5417478400.0 53638400.0 GSM8020164 r1 0:101 A:1459560082;C:1269220844;G:1235271759;T:1453256921;N:168794 101       1459560082 1269220844 1235271759 1453256921 168794 SRX23261704 SRS20163669 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29952 29952 SRR27592977 SRX23261703 SRS20163668 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep8 GSM8020163   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep8 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020163 GSM8020163: deaf1 c207y 2 dpf rep8; Danio rerio; RNA Seq GSM8020163 r1 GSM8020163 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A9_S9_R1_001.fastq.gz fastq 2417886167.0 23939467.0 GSM8020163 r1 0:101 A:657342317;C:558713775;G:547590726;T:654164599;N:74750 101       657342317 558713775 547590726 654164599 74750 SRX23261703 SRS20163668 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29953 29953 SRR27592978 SRX23261702 SRS20163667 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep7 GSM8020162   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep7 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020162 GSM8020162: deaf1 c207y 2 dpf rep7; Danio rerio; RNA Seq GSM8020162 r1 GSM8020162 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A8_S8_R1_001.fastq.gz fastq 3601305288.0 35656488.0 GSM8020162 r1 0:101 A:974139857;C:839029639;G:822572729;T:965450738;N:112325 101       974139857 839029639 822572729 965450738 112325 SRX23261702 SRS20163667 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29954 29954 SRR27592979 SRX23261701 SRS20163666 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep6 GSM8020161   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep6 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous GSM8020161 GSM8020161: deaf1 c207y 2 dpf rep6; Danio rerio; RNA Seq GSM8020161 r1 GSM8020161 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz fastq 2545549965.0 25203465.0 GSM8020161 r1 0:101 A:689302325;C:596907356;G:578571204;T:680690103;N:78977 101       689302325 596907356 578571204 680690103 78977 SRX23261701 SRS20163666 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29955 29955 SRR27592980 SRX23261700 SRS20163665 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep5 GSM8020160   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep5 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020160 GSM8020160: deaf1 c207y 2 dpf rep5; Danio rerio; RNA Seq GSM8020160 r1 GSM8020160 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A5_S5_R1_001.fastq.gz fastq 3102857158.0 30721358.0 GSM8020160 r1 0:101 A:850838897;C:712670459;G:688515516;T:850736210;N:96076 101       850838897 712670459 688515516 850736210 96076 SRX23261700 SRS20163665 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29956 29956 SRR27592981 SRX23261699 SRS20163664 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep4 GSM8020159   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep4 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020159 GSM8020159: deaf1 c207y 2 dpf rep4; Danio rerio; RNA Seq GSM8020159 r1 GSM8020159 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A4_S4_R1_001.fastq.gz fastq 3415651633.0 33818333.0 GSM8020159 r1 0:101 A:933225760;C:786732356;G:770845968;T:924742081;N:105468 101       933225760 786732356 770845968 924742081 105468 SRX23261699 SRS20163664 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29957 29957 SRR27592982 SRX23261698 SRS20163663 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep3 GSM8020158   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep3 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020158 GSM8020158: deaf1 c207y 2 dpf rep3; Danio rerio; RNA Seq GSM8020158 r1 GSM8020158 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A3_S3_R1_001.fastq.gz fastq 3429734972.0 33957772.0 GSM8020158 r1 0:101 A:920850547;C:802940416;G:790735026;T:915103526;N:105457 101       920850547 802940416 790735026 915103526 105457 SRX23261698 SRS20163663 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29958 29958 SRR27592983 SRX23261697 SRS20163662 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep2 GSM8020157   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep2 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020157 GSM8020157: deaf1 c207y 2 dpf rep2; Danio rerio; RNA Seq GSM8020157 r1 GSM8020157 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A2_S2_R1_001.fastq.gz fastq 2810870602.0 27830402.0 GSM8020157 r1 0:101 A:742011214;C:673773327;G:656344142;T:738655690;N:86229 101       742011214 673773327 656344142 738655690 86229 SRX23261697 SRS20163662 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29959 29959 SRR27592984 SRX23261696 SRS20163661 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 c207y 2 dpf rep1 GSM8020156   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous|geo loc name:missing|collection date:missing deaf1 c207y 2 dpf rep1 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y heterozygous GSM8020156 GSM8020156: deaf1 c207y 2 dpf rep1; Danio rerio; RNA Seq GSM8020156 r1 GSM8020156 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-c207y-2dpf-het_A1_S1_R1_001.fastq.gz fastq 4234517819.0 41925919.0 GSM8020156 r1 0:101 A:1104853000;C:1023572758;G:1001000314;T:1104961067;N:130680 101       1104853000 1023572758 1001000314 1104961067 130680 SRX23261696 SRS20163661 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29993 29993 SRR27593018 SRX23261662 SRS20163627 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep13 GSM8020194   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep13 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020194 GSM8020194: deaf1 2 dpf rep13; Danio rerio; RNA Seq GSM8020194 r1 GSM8020194 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D30_S58_R1_001.fastq.gz fastq 4417470800.0 44174708.0 GSM8020194 r1 0:100 A:1088757969;C:1142271720;G:1089301455;T:1097060536;N:79120 100       1088757969 1142271720 1089301455 1097060536 79120 SRX23261662 SRS20163627 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
29994 29994 SRR27593019 SRX23261661 SRS20163626 SRP484215 PRJNA1065838 Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations GSE253405 Transcriptome Analysis Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis.       deaf1 2 dpf rep12 GSM8020193   source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types|geo loc name:missing|collection date:missing deaf1 2 dpf rep12 Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. head with eyes 2 5 heads combined   RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   tissue:head with eyes 2 5 heads combined|genotype:deaf1 23d46i wild types GSM8020193 GSM8020193: deaf1 2 dpf rep12; Danio rerio; RNA Seq GSM8020193 r1 GSM8020193 1 RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP484215   loader:fastq load.py deaf1-23d46i-2dpf-wt_D29_S57_R1_001.fastq.gz fastq 4218209500.0 42182095.0 GSM8020193 r1 0:100 A:1040374012;C:1082175747;G:1042489373;T:1053094232;N:76136 100       1040374012 1082175747 1042489373 1053094232 76136 SRX23261661 SRS20163626 SRA1787174 UMass Chan Medical School UMass Chan Medical School                       B   usable mapping rate illumina novaseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2024-01-16 Hatching Embryo Multi-tissue Multi-system
55877 55877 SRR10863019 SRX7533050 SRS5972252 SRP241074 PRJNA597223 Danio rerio primordial germ cell expression pofiling PRJNA597223 Whole Genome Sequencing Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.     The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.   wt PGCs 2dpf rep3   strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal                 mRNA of Zebrafish: PGCs 2dpf imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6 imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6 Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP241074     imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_06_61_2dpf_PGCs_rep3_S6.R2.fastq.gz fastq fastq 3108720942.0 19675449.0 imb ketting 2018 02 redl SmartSeq 06 61 2dpf PGCs rep3 S6.R1.fastq.gz 0:79 1:79 A:837919918;C:714812252;G:702998193;T:852776390;N:214189 79 79     837919918 714812252 702998193 852776390 214189 SRX7533050 SRS5972252 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.93952 0.93945 0.07277 0.07278 0.66983 0.67221 0.50192 0.50133 79 79 B B biological fallback assumption illumina nextseq unknown poly_a unknown sc single_cell_plate smartseq   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55878 55878 SRR10863020 SRX7533049 SRS5972244 SRP241074 PRJNA597223 Danio rerio primordial germ cell expression pofiling PRJNA597223 Whole Genome Sequencing Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.     The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.   wt PGCs 2dpf rep2   strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal                 mRNA of Zebrafish: PGCs 2dpf imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5 imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5 Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP241074     imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_05_22_2dpf_PGCs_rep2_S5.R2.fastq.gz fastq fastq 3241530370.0 20516015.0 imb ketting 2018 02 redl SmartSeq 05 22 2dpf PGCs rep2 S5.R1.fastq.gz 0:79 1:79 A:861911078;C:762577918;G:730686512;T:886132359;N:222503 79 79     861911078 762577918 730686512 886132359 222503 SRX7533049 SRS5972244 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.93797 0.93734 0.06416 0.06415 0.67004 0.67251 0.50367 0.50353 79 79 B B biological fallback assumption illumina nextseq unknown poly_a unknown sc single_cell_plate smartseq   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55879 55879 SRR10863021 SRX7533048 SRS5972269 SRP241074 PRJNA597223 Danio rerio primordial germ cell expression pofiling PRJNA597223 Whole Genome Sequencing Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.     The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.   wt PGCs 2dpf rep1   strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal                 mRNA of Zebrafish: PGCs 2dpf imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4 imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4 Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP241074     imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_04_07_2dpf_PGCs_rep1_S4.R2.fastq.gz fastq fastq 3363342524.0 21286978.0 imb ketting 2018 02 redl SmartSeq 04 07 2dpf PGCs rep1 S4.R1.fastq.gz 0:79 1:79 A:906938869;C:772810568;G:756589497;T:926768184;N:235406 79 79     906938869 772810568 756589497 926768184 235406 SRX7533048 SRS5972269 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.93588 0.93667 0.11457 0.11483 0.66663 0.66799 0.4795 0.4762 79 79 B B biological fallback assumption illumina nextseq unknown poly_a unknown sc single_cell_plate smartseq   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55893 55893 SRR10863034 SRX7533034 SRS5972259 SRP241074 PRJNA597223 Danio rerio primordial germ cell expression pofiling PRJNA597223 Whole Genome Sequencing Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.     The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.   wt Fish 2dpf rep2   strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 2|BioSampleModel:Model organism or animal                 mRNA of Zebrafish: Fish 2dpf imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16 imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16 Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP241074     imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_16_63_2dpf_Fish_rep2_S16.R2.fastq.gz fastq fastq 3091658206.0 19567457.0 imb ketting 2018 02 redl SmartSeq 16 63 2dpf Fish rep2 S16.R1.fastq.gz 0:79 1:79 A:818837054;C:727836511;G:707557580;T:837216941;N:210120 79 79     818837054 727836511 707557580 837216941 210120 SRX7533034 SRS5972259 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.94667 0.94646 0.08702 0.08692 0.69804 0.70138 0.43628 0.43409 79 79 B B biological fallback assumption illumina nextseq unknown poly_a unknown sc single_cell_plate smartseq   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55894 55894 SRR10863035 SRX7533033 SRS5972258 SRP241074 PRJNA597223 Danio rerio primordial germ cell expression pofiling PRJNA597223 Whole Genome Sequencing Primordial germ cells PGCs are the precursors of germ cells which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes including genes known to induce PGC fate in the mouse are only activated several days post migration. At this same timepoint PGC nuclei become extremely gyrated displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci named PERLs enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly no nuclear Piwi protein could be detected indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.     The vasa:eGFP line Krøvel and Olsen 2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes killed on ice and gently pippeted up and down with a glass pipet and/or a 200µl low retention pipet tip. post visual inspection cell suspension was separated from trunks using a 100 µm siev. Following another 5 15 minutes of digestion FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT washed with PBS resuspended in PBS with 2% FCS put on Ice and immediately subjected to FACS using a 85µm nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at 80°C until library preparation was done.   wt Fish 2dpf rep1   strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:2dpf|dev stage:Long pec stage|sex:not applicable|tissue:whole embryo|biological replicate:replicate 1|BioSampleModel:Model organism or animal                 mRNA of Zebrafish: Fish 2dpf imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15 imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15 Library prep was performed with SmartSeq2 RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 12 PCR cycles.     RNA-Seq TRANSCRIPTOMIC PolyA PAIRED ILLUMINA NextSeq 550   SRP241074     imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R1.fastq.gz imb_ketting_2018_02_redl_SmartSeq_15_02_2dpf_Fish_rep1_S15.R2.fastq.gz fastq fastq 3499876328.0 22151116.0 imb ketting 2018 02 redl SmartSeq 15 02 2dpf Fish rep1 S15.R1.fastq.gz 0:79 1:79 A:931187812;C:820606968;G:796104654;T:951733888;N:243006 79 79     931187812 820606968 796104654 951733888 243006 SRX7533033 SRS5972258 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.94532 0.94537 0.10394 0.10459 0.69489 0.69727 0.4345 0.43676 79 79 B B biological fallback assumption illumina nextseq unknown poly_a unknown sc single_cell_plate smartseq   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
57280 57280 SRR11302641 SRX7908670 SRS6316242 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D22 GSM4410633   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D22 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410633 GSM4410633: zebrafish 990s D22; Danio rerio; RNA Seq GSM4410633   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410633 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D22.bam bam 14952235.0 302958.0 GSM4410633 r1 0:49.35 A:3811307;C:3645371;G:3617661;T:3873396;N:4500 49       3811307 3645371 3617661 3873396 4500 SRX7908670 SRS6316242 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96635   0.06324   0.87769   0.49502   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57281 57281 SRR11302640 SRX7908669 SRS6316243 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D21 GSM4410632   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D21 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410632 GSM4410632: zebrafish 990s D21; Danio rerio; RNA Seq GSM4410632   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410632 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D21.bam bam 12301286.0 248613.0 GSM4410632 r1 0:49.48 A:3216338;C:2918960;G:2899913;T:3262285;N:3790 49       3216338 2918960 2899913 3262285 3790 SRX7908669 SRS6316243 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96446   0.11117   0.9137   0.51287   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57282 57282 SRR11302639 SRX7908668 SRS6316241 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D20 GSM4410631   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D20 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410631 GSM4410631: zebrafish 990s D20; Danio rerio; RNA Seq GSM4410631   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410631 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D20.bam bam 13841010.0 280169.0 GSM4410631 r1 0:49.40 A:3567280;C:3336013;G:3310051;T:3623298;N:4368 49       3567280 3336013 3310051 3623298 4368 SRX7908668 SRS6316241 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96393   0.08232   0.92616   0.49002   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57283 57283 SRR11302638 SRX7908667 SRS6316240 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D2 GSM4410630   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D2 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410630 GSM4410630: zebrafish 990s D2; Danio rerio; RNA Seq GSM4410630   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410630 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D2.bam bam 13249032.0 267250.0 GSM4410630 r1 0:49.58 A:3526925;C:3081325;G:3060212;T:3576643;N:3927 49       3526925 3081325 3060212 3576643 3927 SRX7908667 SRS6316240 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95057   0.1848   0.92504   0.48003   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57284 57284 SRR11302637 SRX7908666 SRS6316237 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D19 GSM4410629   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D19 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410629 GSM4410629: zebrafish 990s D19; Danio rerio; RNA Seq GSM4410629   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410629 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D19.bam bam 24639240.0 496686.0 GSM4410629 r1 0:49.61 A:6408578;C:5886841;G:5845099;T:6491229;N:7493 49       6408578 5886841 5845099 6491229 7493 SRX7908666 SRS6316237 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96339   0.06751   0.91198   0.46563   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57285 57285 SRR11302636 SRX7908665 SRS6316236 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D18 GSM4410628   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D18 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410628 GSM4410628: zebrafish 990s D18; Danio rerio; RNA Seq GSM4410628   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410628 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D18.bam bam 6244321.0 125915.0 GSM4410628 r1 0:49.59 A:1600346;C:1515162;G:1505658;T:1621317;N:1838 49       1600346 1515162 1505658 1621317 1838 SRX7908665 SRS6316236 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96639   0.09462   0.93275   0.51899   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57286 57286 SRR11302635 SRX7908664 SRS6316239 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D17 GSM4410627   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D17 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410627 GSM4410627: zebrafish 990s D17; Danio rerio; RNA Seq GSM4410627   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410627 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D17.bam bam 19546818.0 394040.0 GSM4410627 r1 0:49.61 A:5084961;C:4673304;G:4637984;T:5144779;N:5790 49       5084961 4673304 4637984 5144779 5790 SRX7908664 SRS6316239 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96388   0.09619   0.92419   0.46267   48   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57287 57287 SRR11302634 SRX7908663 SRS6316238 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D16 GSM4410626   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D16 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410626 GSM4410626: zebrafish 990s D16; Danio rerio; RNA Seq GSM4410626   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410626 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D16.bam bam 35129013.0 708869.0 GSM4410626 r1 0:49.56 A:9128792;C:8378350;G:8324629;T:9287068;N:10174 49       9128792 8378350 8324629 9287068 10174 SRX7908663 SRS6316238 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96185   0.07724   0.91597   0.48886   41   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57288 57288 SRR11302633 SRX7908662 SRS6316235 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D15 GSM4410625   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D15 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410625 GSM4410625: zebrafish 990s D15; Danio rerio; RNA Seq GSM4410625   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410625 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D15.bam bam 20555028.0 414281.0 GSM4410625 r1 0:49.62 A:5268027;C:4987353;G:4954575;T:5338793;N:6280 49       5268027 4987353 4954575 5338793 6280 SRX7908662 SRS6316235 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96672   0.07072   0.92295   0.48391   44   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57289 57289 SRR11302632 SRX7908661 SRS6316234 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D14 GSM4410624   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D14 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410624 GSM4410624: zebrafish 990s D14; Danio rerio; RNA Seq GSM4410624   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410624 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D14.bam bam 25155383.0 507445.0 GSM4410624 r1 0:49.57 A:6589687;C:5956715;G:5911932;T:6689599;N:7450 49       6589687 5956715 5911932 6689599 7450 SRX7908661 SRS6316234 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.9592   0.1259   0.91175   0.47661   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57290 57290 SRR11302631 SRX7908660 SRS6316232 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D13 GSM4410623   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D13 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410623 GSM4410623: zebrafish 990s D13; Danio rerio; RNA Seq GSM4410623   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410623 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D13.bam bam 26252350.0 529709.0 GSM4410623 r1 0:49.56 A:6824395;C:6273054;G:6234203;T:6912870;N:7828 49       6824395 6273054 6234203 6912870 7828 SRX7908660 SRS6316232 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96307   0.10084   0.90445   0.47847   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57291 57291 SRR11302630 SRX7908659 SRS6316233 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D12 GSM4410622   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D12 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410622 GSM4410622: zebrafish 990s D12; Danio rerio; RNA Seq GSM4410622   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410622 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D12.bam bam 26274219.0 529278.0 GSM4410622 r1 0:49.64 A:6795815;C:6306706;G:6259822;T:6904582;N:7294 49       6795815 6306706 6259822 6904582 7294 SRX7908659 SRS6316233 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95859   0.10058   0.90106   0.46651   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57292 57292 SRR11302629 SRX7908658 SRS6316231 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D11 GSM4410621   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D11 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410621 GSM4410621: zebrafish 990s D11; Danio rerio; RNA Seq GSM4410621   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410621 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D11.bam bam 10464062.0 211250.0 GSM4410621 r1 0:49.53 A:2687251;C:2533437;G:2512865;T:2727443;N:3066 49       2687251 2533437 2512865 2727443 3066 SRX7908658 SRS6316231 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96414   0.06516   0.94255   0.53005   45   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57293 57293 SRR11302628 SRX7908657 SRS6316229 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D10 GSM4410620   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D10 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410620 GSM4410620: zebrafish 990s D10; Danio rerio; RNA Seq GSM4410620   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410620 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D10.bam bam 22770979.0 459186.0 GSM4410620 r1 0:49.59 A:5826113;C:5533708;G:5495964;T:5908461;N:6733 49       5826113 5533708 5495964 5908461 6733 SRX7908657 SRS6316229 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96785   0.06209   0.90784   0.48004   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57294 57294 SRR11302627 SRX7908656 SRS6316230 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s D1 GSM4410619   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s D1 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410619 GSM4410619: zebrafish 990s D1; Danio rerio; RNA Seq GSM4410619   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410619 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_D1.bam bam 25924183.0 521171.0 GSM4410619 r1 0:49.74 A:6729937;C:6200705;G:6153858;T:6832585;N:7098 49       6729937 6200705 6153858 6832585 7098 SRX7908656 SRS6316230 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96292   0.10401   0.89721   0.48829   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57295 57295 SRR11302626 SRX7908655 SRS6316227 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C9 GSM4410618   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C9 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410618 GSM4410618: zebrafish 990s C9; Danio rerio; RNA Seq GSM4410618   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410618 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C9.bam bam 24266046.0 489282.0 GSM4410618 r1 0:49.60 A:6303157;C:5796448;G:5758377;T:6400971;N:7093 49       6303157 5796448 5758377 6400971 7093 SRX7908655 SRS6316227 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96377   0.09952   0.93604   0.47909   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57296 57296 SRR11302625 SRX7908654 SRS6316228 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C8 GSM4410617   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C8 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410617 GSM4410617: zebrafish 990s C8; Danio rerio; RNA Seq GSM4410617   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410617 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C8.bam bam 21899008.0 441712.0 GSM4410617 r1 0:49.58 A:5747348;C:5177667;G:5136928;T:5830424;N:6641 49       5747348 5177667 5136928 5830424 6641 SRX7908654 SRS6316228 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95958   0.13065   0.92216   0.46914   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57297 57297 SRR11302624 SRX7908653 SRS6316226 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C7 GSM4410616   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C7 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410616 GSM4410616: zebrafish 990s C7; Danio rerio; RNA Seq GSM4410616   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410616 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C7.bam bam 28404846.0 573859.0 GSM4410616 r1 0:49.50 A:7235244;C:6926753;G:6877946;T:7356336;N:8567 49       7235244 6926753 6877946 7356336 8567 SRX7908653 SRS6316226 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96435   0.06783   0.91492   0.48294   42   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57298 57298 SRR11302623 SRX7908652 SRS6316224 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C6 GSM4410615   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C6 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410615 GSM4410615: zebrafish 990s C6; Danio rerio; RNA Seq GSM4410615   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410615 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C6.bam bam 18860719.0 381549.0 GSM4410615 r1 0:49.43 A:5074635;C:4333167;G:4301649;T:5145437;N:5831 49       5074635 4333167 4301649 5145437 5831 SRX7908652 SRS6316224 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95523   0.16234   0.90329   0.47409   41   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57299 57299 SRR11302622 SRX7908651 SRS6316225 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C5 GSM4410614   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C5 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410614 GSM4410614: zebrafish 990s C5; Danio rerio; RNA Seq GSM4410614   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410614 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C5.bam bam 15089981.0 304859.0 GSM4410614 r1 0:49.50 A:3951385;C:3573935;G:3555893;T:4003894;N:4874 49       3951385 3573935 3555893 4003894 4874 SRX7908651 SRS6316225 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96352   0.17134   0.93265   0.47004   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57300 57300 SRR11302621 SRX7908650 SRS6316222 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C4 GSM4410613   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C4 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410613 GSM4410613: zebrafish 990s C4; Danio rerio; RNA Seq GSM4410613   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410613 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C4.bam bam 19269405.0 388669.0 GSM4410613 r1 0:49.58 A:5084174;C:4527015;G:4489207;T:5163246;N:5763 49       5084174 4527015 4489207 5163246 5763 SRX7908650 SRS6316222 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95519   0.12584   0.91977   0.48712   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57301 57301 SRR11302620 SRX7908649 SRS6316223 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C3 GSM4410612   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C3 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410612 GSM4410612: zebrafish 990s C3; Danio rerio; RNA Seq GSM4410612   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410612 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C3.bam bam 26296146.0 529798.0 GSM4410612 r1 0:49.63 A:6879183;C:6235952;G:6187938;T:6985257;N:7816 49       6879183 6235952 6187938 6985257 7816 SRX7908649 SRS6316223 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.9614   0.13063   0.92693   0.48691   44   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57302 57302 SRR11302619 SRX7908648 SRS6316221 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C24 GSM4410611   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C24 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410611 GSM4410611: zebrafish 990s C24; Danio rerio; RNA Seq GSM4410611   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410611 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C24.bam bam 20420608.0 411528.0 GSM4410611 r1 0:49.62 A:5331504;C:4853719;G:4820428;T:5408957;N:6000 49       5331504 4853719 4820428 5408957 6000 SRX7908648 SRS6316221 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96386   0.11067   0.93474   0.44648   42   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57303 57303 SRR11302618 SRX7908647 SRS6316219 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C23 GSM4410610   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C23 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410610 GSM4410610: zebrafish 990s C23; Danio rerio; RNA Seq GSM4410610   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410610 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C23.bam bam 35047445.0 705646.0 GSM4410610 r1 0:49.67 A:9165559;C:8316903;G:8242039;T:9312819;N:10125 49       9165559 8316903 8242039 9312819 10125 SRX7908647 SRS6316219 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95667   0.08618   0.90662   0.48076   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57304 57304 SRR11302617 SRX7908646 SRS6316220 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C22 GSM4410609   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C22 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410609 GSM4410609: zebrafish 990s C22; Danio rerio; RNA Seq GSM4410609   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410609 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C22.bam bam 26040133.0 524602.0 GSM4410609 r1 0:49.64 A:6788556;C:6199193;G:6157557;T:6887011;N:7816 49       6788556 6199193 6157557 6887011 7816 SRX7908646 SRS6316220 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.95869   0.11718   0.9027   0.4912   48   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57305 57305 SRR11302616 SRX7908645 SRS6316217 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C21 GSM4410608   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C21 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410608 GSM4410608: zebrafish 990s C21; Danio rerio; RNA Seq GSM4410608   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410608 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C21.bam bam 27771299.0 564142.0 GSM4410608 r1 0:49.23 A:7277456;C:6567924;G:6520282;T:7397263;N:8374 49       7277456 6567924 6520282 7397263 8374 SRX7908645 SRS6316217 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96216   0.08311   0.92214   0.484   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57306 57306 SRR11302615 SRX7908644 SRS6316218 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C20 GSM4410607   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C20 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410607 GSM4410607: zebrafish 990s C20; Danio rerio; RNA Seq GSM4410607   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410607 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C20.bam bam 12727564.0 257166.0 GSM4410607 r1 0:49.49 A:3253378;C:3091074;G:3068783;T:3310426;N:3903 49       3253378 3091074 3068783 3310426 3903 SRX7908644 SRS6316218 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96581   0.09966   0.92336   0.46559   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57307 57307 SRR11302614 SRX7908643 SRS6316216 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C2 GSM4410606   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C2 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410606 GSM4410606: zebrafish 990s C2; Danio rerio; RNA Seq GSM4410606   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410606 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C2.bam bam 24641347.0 496145.0 GSM4410606 r1 0:49.67 A:6362402;C:5928362;G:5889128;T:6454430;N:7025 49       6362402 5928362 5889128 6454430 7025 SRX7908643 SRS6316216 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96422   0.09577   0.9095   0.47689   41   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57308 57308 SRR11302613 SRX7908642 SRS6316215 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C19 GSM4410605   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C19 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410605 GSM4410605: zebrafish 990s C19; Danio rerio; RNA Seq GSM4410605   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410605 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C19.bam bam 35386657.0 712451.0 GSM4410605 r1 0:49.67 A:9180689;C:8467349;G:8402491;T:9325656;N:10472 49       9180689 8467349 8402491 9325656 10472 SRX7908642 SRS6316215 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96283   0.1015   0.87852   0.47362   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57309 57309 SRR11302612 SRX7908641 SRS6316214 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C18 GSM4410604   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C18 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410604 GSM4410604: zebrafish 990s C18; Danio rerio; RNA Seq GSM4410604   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410604 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C18.bam bam 17769590.0 358461.0 GSM4410604 r1 0:49.57 A:4590943;C:4269740;G:4239656;T:4663920;N:5331 49       4590943 4269740 4239656 4663920 5331 SRX7908641 SRS6316214 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.9647   0.09031   0.93288   0.48597   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57310 57310 SRR11302611 SRX7908640 SRS6316213 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C17 GSM4410603   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C17 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410603 GSM4410603: zebrafish 990s C17; Danio rerio; RNA Seq GSM4410603   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410603 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C17.bam bam 32426584.0 653000.0 GSM4410603 r1 0:49.66 A:8461669;C:7712485;G:7651317;T:8591564;N:9549 49       8461669 7712485 7651317 8591564 9549 SRX7908640 SRS6316213 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.9592   0.08874   0.91259   0.49461   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57311 57311 SRR11302610 SRX7908639 SRS6316212 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C16 GSM4410602   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C16 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410602 GSM4410602: zebrafish 990s C16; Danio rerio; RNA Seq GSM4410602   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410602 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C16.bam bam 25635088.0 516511.0 GSM4410602 r1 0:49.63 A:6592405;C:6192402;G:6144035;T:6698710;N:7536 49       6592405 6192402 6144035 6698710 7536 SRX7908639 SRS6316212 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96488   0.06936   0.90636   0.48394   36   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure
57312 57312 SRR11302609 SRX7908638 SRS6316211 SRP252691 PRJNA612443 Specific fibroblast subpopulations and neuronal structures serve as local sources of Vegfc processing components during lymphangiogenesis GSE146923 Transcriptome Analysis Proteolytical processing of the growth factor VEGFC through the concerted activity of CCBE1 and ADAMTS3 is required for lymphatic development to occur. How these factors act together in time and space and which cell types produce these factors is not understood. Here we assess the function of Adamts3 and the related protease Adamts14 during zebrafish lymphangiogenesis and show both proteins to be able to process Vegfc. Only the simultaneous loss of both protein functions results in lymphatic defects identical to vegfc loss of function situations. Cell transplantation experiments demonstrate neuronal structures and/or fibroblasts to constitute cellular sources not only for both proteases but also for Ccbe1 and Vegfc. We further show that it is the local restriction of Vegfc maturation which is needed to trigger normal lymphatic sprouting and directional migration. Our data provide a single cell resolution model for establishing secretion and processing hubs for Vegfc during developmental lymphangiogenesis Overall design: single cell transcriptomes were generated of individual cells captured from 48 hpf old zebrafish embryos by single cell RNA sequencing   pubmed:32483144   zebrafish 990s C15 GSM4410601   source name:zebrafish|tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf zebrafish 990s C15 bcl2fastq demultiplexing sequenced reads were trimmed for adaptor sequence and then mapped to the zebrafish reference genome danRer11 using TapHat2 Bowtie2. raw read counts per gene were calculated using featureCounts from subread for analysis all raw counts from all cells of each of the three sample plates plate 123 plate 989 plate 990 were combined into one expression matrix file counts data was processed and analyzed using velocyto SingleCellExperiment and pagoda2 packages in R software Genome build: GRCz11 danRer11 Supplementary files format and content: tab deliminated txt file as expression matrix including non normalized counts of all samples zebrafish   FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol   tissue:embryo trunk|starin:vegfc:Gal4FF;UASGFP; kdrl:mCherry|age:48 hpf GSM4410601 GSM4410601: zebrafish 990s C15; Danio rerio; RNA Seq GSM4410601   1 FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin EDTA and 10U Dnase I for 30min at 30°C RNA libraries were prepared using standard SmartSeq2 protocol GEO Accession:GSM4410601 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 3000   SRP252691   intentional duplicate|dangling references:treat as unmapped zebrafish_990s_C15.bam bam 24612894.0 495477.0 GSM4410601 r1 0:49.68 A:6387972;C:5887843;G:5848486;T:6481347;N:7246 49       6387972 5887843 5848486 6481347 7246 SRX7908638 SRS6316211 SRA1054549 GEO Betsholtz, ICMC - MedH, Karolinska Institutet 1 0.96143   0.11709   0.91139   0.48454   40   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   Sweden 2020-03-13 Hatching Embryo Trunk Surface Structure

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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");;