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14 rows where devstage_curation = "Hatching" and experiment.library_selection = "unspecified"

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tissue_curation 3

tissue_curation_coarse 2

technology 2

experiment.library_strategy 2

experiment.library_layout 2

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • unspecified · 14 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Hatching · 14 ✖
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
8063 8063 ERR022487 ERX008918 ERS012707 ERP000400 PRJEB2333 Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E-MTAB-434 Other         E MTAB 308:Zebrafish embryo 2 dpf 2 SAMEA898403 Wellcome Sanger Institute Age:2 days|Alias:E MTAB 308:Zebrafish embryo 2 dpf 2|Broker name:ArrayExpress|Description:Protocols: Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments.|DevelopmentalStage:embryo|INSDC center alias:SC|INSDC center name:Wellcome Sanger Institute|INSDC first public:2010 08 19T15:57:35Z|INSDC last update:2018 03 08T15:25:04Z|INSDC status:public|InitialTimePoint:fertilization|OrganismPart:whole organism|SRA accession:ERS012707|Sample Name:ERS012707|Sex:unknown sex|StrainOrLine:Tuebingen|Title:Danio rerio                 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer E MTAB 434:sequencing of Zebrafish embryo 2 dpf RNA from Zebrafish embryo 2 dpf Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer Zebrafish embyos or tissues were collected from a Tuebingen strain incross and grown at 28 C. Collected samples were snap frozen on dry ice and stored at 70 C Total RNA was extracted using Trizol Reagent Invitrogen following the manufacturer's instructions. Pellets were resuspended RNase free 10 mM Tris pH 7.5 and the RNA was quantified using a NanoDrop ND 1000 Spectrophotometer Axon Instruments. Total RNA was made into an RNAseq Illumina library following the manufacturer's protocol including a DNase treatment between to 2 rounds of polyA pull down. The libraries have fragment size of 250 to 300 bp. Experimental Factor: AGE:2 d|Experimental Factor: DEVELPOMENTAL STAGE:embryo|Experimental Factor: ORGANISM PART:whole organism FL-cDNA TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina Genome Analyzer II   ERP000400 Illumina Genome Analyzer II paired end sequencing; Sequencing the Zebrafish transcriptome form a range of tissues and developmental stages using the Illumina Genome Analyzer ENA FIRST PUBLIC:2011 03 10|ENA LAST UPDATE:2018 11 16 5141_5.srf srf 4321796696.0 28432873.0 E MTAB 434:5141 5.srf 0:76 1:76 A:1185782721;C:976784015;G:973264244;T:1178952292;N:7013424 76 76     1185782721 976784015 973264244 1178952292 7013424 ERX008918 ERS012707 ERA015179 SC|Wellcome Trust Sanger Institute SC|Wellcome Trust Sanger Institute 2 0.96001 0.95851 0.15373 0.15636 0.69051 0.69576 0.47409 0.47525 76 76 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   United Kingdom 2010-08-19 Hatching Embryo Whole Organism All anatomical structures
54190 54190 SRR10095966 SRX6828143 SRS5370318 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         2b   strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 2b 2b 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 4000   SRP221273   loader:latf load olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 100194025377.0 630151103.0 2b.gz 0:26 1:133 A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462 26 133     27235389395 22388810842 23041272930 27513445748 15106462 SRX6828143 SRS5370318 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.0127 0.95456 0.00215 0.09469 0.97463 0.79308 0.43287 0.50046 26 133 T B sc-like readlen illumina hiseq_era unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Hatching Embryo Whole Organism All anatomical structures
54191 54191 SRR10095967 SRX6828142 SRS5370317 SRP221273 PRJNA564810 A Single Cell Transcriptome Atlas for Zebrafish Development PRJNA564810 Other The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.         2a   strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal                 scRNA seq of whole zebrafish embryos 2a 2a 10X v2 chromium cDNA library     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA NextSeq 500   SRP221273   loader:latf load 2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 30654488793.0 192795527.0 2a.gz 0:26 1:133 A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245 26 133     8922702024 6370087682 7321183700 8019014142 21501245 SRX6828142 SRS5370317 SRA960102 University of Oregon|Institute of Neuroscience University of Oregon 2 0.00427 0.91705 0.00106 0.08701 0.98999 0.8198 0.35255 0.50555 26 133 T B sc-like readlen illumina nextseq unknown unknown unknown sc single_cell_droplet 10x   United States 2019-12-10 Hatching Embryo Whole Organism All anatomical structures
62507 62507 SRR13234623 SRX9666703 SRS7865638 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48h miR 430 pA AGN000156   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000144|replicate ref:AGN000156|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf + miR 430 polyA AGR000210 AGR000210 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000210_R1.fastq.gz fastq 2609702212.0 34338187.0 AGR000210 R1.fastq.gz 0:76 1:0 A:704577933;C:585211587;G:576153508;T:743579979;N:179205 76 0     704577933 585211587 576153508 743579979 179205 SRX9666703 SRS7865638 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93632   0.13425   0.68489   0.46247   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62508 62508 SRR13234624 SRX9666702 SRS7865640 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48h pA AGN000155   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdrosha|strain maternal:drosha / |strain paternal:drosha / |molecule:RNA|selection:pA|sample ref:AGS000143|replicate ref:AGN000155|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdrosha 48hpf polyA AGR000209 AGR000209 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000209_R1.fastq.gz fastq 2762255872.0 36345472.0 AGR000209 R1.fastq.gz 0:76 1:0 A:744803398;C:616941583;G:611018882;T:789301931;N:190078 76 0     744803398 616941583 611018882 789301931 190078 SRX9666702 SRS7865640 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93333   0.1447   0.67556   0.46613   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62509 62509 SRR13234625 SRX9666701 SRS7865639 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf + miR 430 polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48h miR 430 pA AGN000154   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |treatment:miR 430|molecule:RNA|selection:pA|sample ref:AGS000142|replicate ref:AGN000154|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf + miR 430 polyA AGR000208 AGR000208 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000208_R1.fastq.gz fastq 2256650140.0 29692765.0 AGR000208 R1.fastq.gz 0:76 1:0 A:605316845;C:506931236;G:499614551;T:644626383;N:161125 76 0     605316845 506931236 499614551 644626383 161125 SRX9666701 SRS7865639 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93484   0.1382   0.68753   0.46979   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62510 62510 SRR13234626 SRX9666700 SRS7865637 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48h pA AGN000153   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|genotype:MZdicer|strain maternal:dicer / |strain paternal:dicer / |molecule:RNA|selection:pA|sample ref:AGS000141|replicate ref:AGN000153|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 MZdicer 48hpf polyA AGR000207 AGR000207 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000207_R1.fastq.gz fastq 3097923020.0 40762145.0 AGR000207 R1.fastq.gz 0:76 1:0 A:867547957;C:671005273;G:664584552;T:894570865;N:214373 76 0     867547957 671005273 664584552 894570865 214373 SRX9666700 SRS7865637 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.92558   0.17346   0.68763   0.47572   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
62511 62511 SRR13234627 SRX9666699 SRS7865635 SRP297464 PRJNA683902 Ythdf m6A readers function redundantly during zebrafish development PRJNA683902 Other During the maternal to zygotic transition MZT multiple mechanisms precisely control massive decay of maternal mRNAs. N6 methyladenosine m6A is known to regulate mRNA decay yet how this modification promotes maternal transcript degradation remains unclear. Here we find that m6A promotes maternal mRNA deadenylation. Yet genetic loss of m6A readers Ythdf2 and Ythdf3 did not impact global maternal mRNA clearance zygotic genome activation or the onset of gastrulation challenging the view that Ythdf2 alone is critical to developmental timing. We reveal that Ythdf proteins function redundantly during zebrafish oogenesis and development as double Ythdf2 and Ythdf3 deletion prevented female gonad formation and triple Ythdf mutants were lethal. Finally we show that the microRNA miR 430 functions additively with methylation to promote degradation of common transcript targets. Together these findings reveal that m6A facilitates maternal mRNA deadenylation and that multiple pathways and readers act in concert to mediate these effects of methylation on RNA stability.       WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 48hpf polyA WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 WT 48h pA AGN000152   strain:TU/AB|age:48.0|sex:pooled male and female|tissue:embryo|strain maternal:wild type|strain paternal:wild type|molecule:RNA|selection:pA|sample ref:AGS000140|replicate ref:AGN000152|replicate order:1|BioSampleModel:Model organism or animal                 WT MZdrosha MZdicer mRNA 6 24 48 hpf pA & R0 wild type 48hpf polyA AGR000206 AGR000206 RNA     RNA-Seq TRANSCRIPTOMIC unspecified SINGLE ILLUMINA Illumina HiSeq 2000   SRP297464     AGR000206_R1.fastq.gz fastq 2629388112.0 34597212.0 AGR000206 R1.fastq.gz 0:76 1:0 A:705900102;C:587010373;G:584434557;T:751862507;N:180573 76 0     705900102 587010373 584434557 751862507 180573 SRX9666699 SRS7865635 SRA1169659 Yale_Giraldez|Genetics Yale_Giraldez_Group 1 0.93679   0.13092   0.68521   0.44617   76   B   usable mapping rate illumina hiseq_era unknown poly_a unknown bulk unknown unknown   United States 2020-12-10 Hatching Embryo Embryo Imprecise All anatomical structures
66222 66222 SRR16148348 SRX12433220 SRS10400589 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 3 RNAseq Gli3 /   RNAseq Gli3KO 3   strain:Gli3 / ex5 3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 6 6 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3KO3_aligned.sorted.bam bam 5067915101.0 25431299.0 Gli3KO3 aligned.sorted.bam 0:99.63 1:99.65 A:1368455893;C:1172445678;G:1173478123;T:1353535407;N:0 99 99     1368455893 1172445678 1173478123 1353535407 0 SRX12433220 SRS10400589 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95469 0.95749 0.09504 0.09606 0.73951 0.73963 0.54439 0.54442 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66223 66223 SRR16148349 SRX12433219 SRS10400587 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 2 RNAseq Gli3 /   RNAseq Gli3KO 2   strain:Gli3 / ex5 2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 5 5 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3KO2_aligned.cordinatesort.bam bam 10961381631.0 54976705.0 V300059050 Gli3KO2 aligned.cordinatesort.bam 0:99.70 1:99.68 A:2988819475;C:2499700971;G:2467906402;T:3004531404;N:423379 99 99     2988819475 2499700971 2467906402 3004531404 423379 SRX12433219 SRS10400587 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94015 0.9439 0.12356 0.12485 0.75315 0.75304 0.51072 0.50897 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66224 66224 SRR16148350 SRX12433218 SRS10400586 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 1 RNAseq Gli3 /   RNAseq Gli3KO 1   strain:Gli3 / ex5 1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: Gli3 / EGFP cells 4 4 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3KO1_aligned.cordinatesort.bam bam 10204176056.0 51177828.0 V300059050 Gli3KO1 aligned.cordinatesort.bam 0:99.68 1:99.71 A:2761524632;C:2342024573;G:2322758345;T:2777476126;N:392380 99 99     2761524632 2342024573 2322758345 2777476126 392380 SRX12433218 SRS10400586 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94248 0.9466 0.11206 0.11246 0.73634 0.73582 0.50038 0.49971 100 91 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66225 66225 SRR16148351 SRX12433217 SRS10400585 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 3 RNAseq WT   RNAseq WT 3   strain:WT3|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 3 3 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3WT3_aligned.sorted.bam bam 6055778800.0 30391313.0 Gli3WT3 aligned.sorted.bam 0:99.60 1:99.66 A:1632778751;C:1402895889;G:1402788250;T:1617315910;N:0 99 99     1632778751 1402895889 1402788250 1617315910 0 SRX12433217 SRS10400585 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95971 0.96273 0.09206 0.09219 0.72458 0.72391 0.55162 0.55278 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66226 66226 SRR16148353 SRX12433215 SRS10400584 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 2 RNAseq WT   RNAseq WT 2   strain:WT2|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 2 2 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 Gli3WT2_aligned.sorted.bam bam 6030526704.0 30274232.0 Gli3WT2 aligned.sorted.bam 0:99.58 1:99.62 A:1627670320;C:1395587022;G:1395639693;T:1611629669;N:0 99 99     1627670320 1395587022 1395639693 1611629669 0 SRX12433215 SRS10400584 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.95942 0.96186 0.08632 0.08652 0.72671 0.72732 0.53408 0.55623 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise
66227 66227 SRR16148354 SRX12433214 SRS10400582 SRP339629 PRJNA767802 RNA seq and ATAC seq of WT and Gli3 / zebrafish PRJNA767802 Other WE collected EGFP cells Gli3 positive cells from CNE14:EGFP transgenic zebrafish at 55 hpf. RNA seq was performed on 3 wildtype WT and 3 Gli3 / replicates. ATAC seq was performed using EGFP cells from 3 WT replicates and using whole embryo cells from 2 WT replicates. These files reveal presumable Gli3 target genes.     Replicate 1 RNAseq WT   RNAseq WT 1   strain:WT1|dev stage:55hpf|sex:NA|tissue:EGFP cells|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: WT EGFP cells 1 1 Total RNA was immediately extracted from isolated 100 000 EGFP positive cells by FACS using Trizol Invitrogen. Briefly the cell suspension was mixed with 1ml of Trizol by vigorous Vortexing and kept for 5 minutes at the room temperature. The mixed solution was centrifuged and the supernatant was recovered to a new tube. 0.2 ml chloroform was added vigorously vortexed and centrifuged for 15 minutes. The supernatant was mixed with 0.5 ml of isopropanol kept for 10 minutes at room temperature and centrifuged for 15 minutes. The precipitated RNA was washed by 70% ethanol and reconstituted in 30 ul water. The RNA solution was submitted to Novogene CA USA converted to sequencing library and sequenced.     RNA-Seq TRANSCRIPTOMIC unspecified PAIRED ILLUMINA Illumina HiSeq 4000   SRP339629   assembly:GRCz11 V300059050_Gli3WT_aligned.cordinatesort.bam bam 8907848854.0 44671741.0 V300059050 Gli3WT aligned.cordinatesort.bam 0:99.68 1:99.73 A:2444869517;C:2007841709;G:1991672704;T:2463143463;N:321461 99 99     2444869517 2007841709 1991672704 2463143463 321461 SRX12433214 SRS10400582 SRA1303956 Rutgers University|Genetics Rutgers University 2 0.94004 0.94329 0.13907 0.13978 0.74943 0.74897 0.507 0.5105 100 100 B B biological fallback assumption illumina hiseq_era unknown unknown unknown bulk unknown unknown   United States 2021-10-01 Hatching Embryo Undetermined Embryo Imprecise

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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");;