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9 rows where devstage_curation = "Segmentation" and tissue_curation = "Head"

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  • Head · 9 ✖

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  • Segmentation · 9 ✖
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
67086 67086 SRR19619600 SRX15670299 SRS13368594 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxMo 3 GSM6234411   source name:head|tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino vsxMo 3 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Assembly: GRCz10 Supplementary files format and content: fpkm values cufflinks output head vsx2 morpholino was injected in zebrafish fertilized embryos at xxx cell stage. Injected embryos were kept in E3 medium at 28 °C until 18 hpf. Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino GSM6234411 GSM6234411: vsxMo 3; Danio rerio; RNA Seq GSM6234411   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM6234411 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-6_R1.fastq.gz 180309_SNK268_B_L006_AJSG-6_R2.fastq.gz fastq fastq 13022904900.0 43409683.0 GSM6234411 r1 0:150 1:150 A:3543465307;C:2968369623;G:3091890175;T:3416901711;N:2278084 150 150     3543465307 2968369623 3091890175 3416901711 2278084 SRX15670299 SRS13368594 SRA1335663 GEO IRCSS-SDN 2 0.90866 0.90989 0.27311 0.27129 0.71827 0.72279 0.4496 0.45021 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2022-06-10 Segmentation Embryo Head Nervous System
67087 67087 SRR19619599 SRX15670298 SRS13368593 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxMo 2 GSM6234410   source name:head|tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino vsxMo 2 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Assembly: GRCz10 Supplementary files format and content: fpkm values cufflinks output head vsx2 morpholino was injected in zebrafish fertilized embryos at xxx cell stage. Injected embryos were kept in E3 medium at 28 °C until 18 hpf. Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino GSM6234410 GSM6234410: vsxMo 2; Danio rerio; RNA Seq GSM6234410   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM6234410 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-5_R1.fastq.gz 180309_SNK268_B_L006_AJSG-5_R2.fastq.gz fastq fastq 11646553800.0 38821846.0 GSM6234410 r1 0:150 1:150 A:3265577403;C:2562971744;G:2684296991;T:3131663484;N:2044178 150 150     3265577403 2562971744 2684296991 3131663484 2044178 SRX15670298 SRS13368593 SRA1335663 GEO IRCSS-SDN 2 0.8855 0.88663 0.36271 0.36075 0.71366 0.71693 0.44946 0.46412 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2022-06-10 Segmentation Embryo Head Nervous System
67088 67088 SRR19619598 SRX15670297 SRS13368595 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxMo 1 GSM6234409   source name:head|tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino vsxMo 1 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Assembly: GRCz10 Supplementary files format and content: fpkm values cufflinks output head vsx2 morpholino was injected in zebrafish fertilized embryos at xxx cell stage. Injected embryos were kept in E3 medium at 28 °C until 18 hpf. Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage tissue:head|developmental stage:18 hpf|treatment:injection with vsx2 morpholino GSM6234409 GSM6234409: vsxMo 1; Danio rerio; RNA Seq GSM6234409   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM6234409 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-4_R1.fastq.gz 180309_SNK268_B_L006_AJSG-4_R2.fastq.gz fastq fastq 12079011900.0 40263373.0 GSM6234409 r1 0:150 1:150 A:3350754923;C:2683917946;G:2793980843;T:3248257470;N:2100718 150 150     3350754923 2683917946 2793980843 3248257470 2100718 SRX15670297 SRS13368595 SRA1335663 GEO IRCSS-SDN 2 0.8955 0.89612 0.31925 0.31609 0.71411 0.71855 0.44709 0.45446 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2022-06-10 Segmentation Embryo Head Nervous System
67089 67089 SRR17055699 SRX13244628 SRS11168047 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxKO 3 GSM5706509   tissue:head|developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / vsxKO 3 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / GSM5706509 GSM5706509: vsxKO 3; Danio rerio; RNA Seq GSM5706509   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706509 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-3_R1.fastq.gz 180309_SNK268_B_L006_AJSG-3_R2.fastq.gz fastq fastq 11343480300.0 37811601.0 GSM5706509 r1 0:150 1:150 A:3143672530;C:2530724823;G:2635492767;T:3031592697;N:1997483 150 150     3143672530 2530724823 2635492767 3031592697 1997483 SRX13244628 SRS11168047 SRA1335663 GEO IRCSS-SDN 2 0.89654 0.89772 0.31642 0.31441 0.71074 0.71415 0.45145 0.4612 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System
67090 67090 SRR17055698 SRX13244627 SRS11168046 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxKO 2 GSM5706508   tissue:head|developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / vsxKO 2 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / GSM5706508 GSM5706508: vsxKO 2; Danio rerio; RNA Seq GSM5706508   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706508 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-2_R1.fastq.gz 180309_SNK268_B_L006_AJSG-2_R2.fastq.gz fastq fastq 11015571600.0 36718572.0 GSM5706508 r1 0:150 1:150 A:3054551364;C:2445454870;G:2553423245;T:2960209070;N:1933051 150 150     3054551364 2445454870 2553423245 2960209070 1933051 SRX13244627 SRS11168046 SRA1335663 GEO IRCSS-SDN 2 0.89808 0.90056 0.31264 0.31148 0.70861 0.71281 0.44675 0.45992 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System
67091 67091 SRR17055697 SRX13244626 SRS11168045 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   vsxKO 1 GSM5706507   tissue:head|developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / vsxKO 1 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:vsx1 / ; vsx2 / GSM5706507 GSM5706507: vsxKO 1; Danio rerio; RNA Seq GSM5706507   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706507 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-1_R1.fastq.gz 180309_SNK268_B_L006_AJSG-1_R2.fastq.gz fastq fastq 13449666000.0 44832220.0 GSM5706507 r1 0:150 1:150 A:3712403217;C:3003635125;G:3122344123;T:3608948299;N:2335236 150 150     3712403217 3003635125 3122344123 3608948299 2335236 SRX13244626 SRS11168045 SRA1335663 GEO IRCSS-SDN 2 0.89955 0.89936 0.30611 0.30338 0.70954 0.71366 0.45041 0.44415 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System
67092 67092 SRR17055696 SRX13244625 SRS11168044 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   WT 3 GSM5706506   tissue:head|developmental stage:18 hpf|genotype:WT WT 3 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:WT GSM5706506 GSM5706506: WT 3; Danio rerio; RNA Seq GSM5706506   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706506 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-9_R1.fastq.gz 180309_SNK268_B_L006_AJSG-9_R2.fastq.gz fastq fastq 12432650400.0 41442168.0 GSM5706506 r1 0:150 1:150 A:3448182359;C:2758942731;G:2873246550;T:3350119390;N:2159370 150 150     3448182359 2758942731 2873246550 3350119390 2159370 SRX13244625 SRS11168044 SRA1335663 GEO IRCSS-SDN 2 0.89621 0.89719 0.31128 0.30857 0.71236 0.71585 0.45013 0.45774 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System
67093 67093 SRR17055695 SRX13244624 SRS11168043 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   WT 2 GSM5706505   tissue:head|developmental stage:18 hpf|genotype:WT WT 2 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:WT GSM5706505 GSM5706505: WT 2; Danio rerio; RNA Seq GSM5706505   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706505 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-8_R1.fastq.gz 180309_SNK268_B_L006_AJSG-8_R2.fastq.gz fastq fastq 10022151000.0 33407170.0 GSM5706505 r1 0:150 1:150 A:2783012342;C:2226043152;G:2325308404;T:2686033359;N:1753743 150 150     2783012342 2226043152 2325308404 2686033359 1753743 SRX13244624 SRS11168043 SRA1335663 GEO IRCSS-SDN 2 0.89866 0.89944 0.3145 0.31163 0.71476 0.7189 0.45528 0.4623 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System
67094 67094 SRR17055694 SRX13244623 SRS11168042 SRP348277 PRJNA784298 Mutation of Vsx genes in zebrafish highlights the robustness of the retinal specification network [RNA Seq] GSE189737 Transcriptome Analysis Genetic studies in human and mice have established a dual role for Vsx genes in retina development: an early function in progenitors' specification and a later requirement for bipolar cells fate determination. Despite their conserved expression patterns it is currently unclear to which extent Vsx functions are also conserved across vertebrates as mutant models are available only in mammals. To gain insight into vsx function in teleosts we have generated vsx1 and vsx2 CRISPR Cas9 double knockouts vsxKO in zebrafish. Our electrophysiological and histological analyses indicate severe visual impairment and bipolar cells depletion in vsxKO larvae with retinal precursors being rerouted towards photoreceptors or Müller glia fates. Surprisingly neural retina is properly specified and maintained in mutant embryos which do not display microphthalmia. We show that although important cis regulatory remodelling occurs in vsxKO retinas during early specification this has little impact at a transcriptomic level. Our observations point to genetic redundancy as an important mechanism sustaining the integrity of the retinal specification network and to Vsx genes regulatory weight varying substantially among vertebrate species. Overall design: Head of zebrafish embryos at 18 hpf were dissected and used for RNA extraction. Tails were used for genotyping. parent bioproject:PRJNA784293 pubmed:37227126   WT 1 GSM5706504   tissue:head|developmental stage:18 hpf|genotype:WT WT 1 Each sample was mapped against the index genome built from GRCz10 assembly using Hisat2 Kim et al. 2015 The aligned read SAM files were assembled into transcripts their abundance was estimated and tested for differential expression by Cufflinks v2.2.1Trapnell et al. 2012 Genome build: GRCz10 Supplementary files format and content: fpkm values cufflinks output head   Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA zebrafish embryos were kept in E3 medium at 28°C until 18 hpf stage developmental stage:18 hpf|genotype:WT GSM5706504 GSM5706504: WT 1; Danio rerio; RNA Seq GSM5706504   1 Trizol extraction as manufacturer's instruction; DNAse treatment RiboZero stranded RNA GEO Accession:GSM5706504 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP348277     180309_SNK268_B_L006_AJSG-7_R1.fastq.gz 180309_SNK268_B_L006_AJSG-7_R2.fastq.gz fastq fastq 12083337300.0 40277791.0 GSM5706504 r1 0:150 1:150 A:3379986050;C:2659960500;G:2767236627;T:3274019596;N:2134527 150 150     3379986050 2659960500 2767236627 3274019596 2134527 SRX13244623 SRS11168042 SRA1335663 GEO IRCSS-SDN 2 0.89628 0.8988 0.32007 0.31887 0.70899 0.71246 0.45974 0.46528 150 150 B B biological fallback assumption illumina hiseq_era unknown rrna_depletion ribozero bulk unknown unknown   Italy 2021-11-28 Segmentation Embryo Head Nervous System

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