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75 rows where devstage_curation = "Hatching" and experiment.library_selection = "RANDOM"

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tissue_curation 4

tissue_curation_coarse 3

technology 2

experiment.library_strategy 2

experiment.library_layout 2

experiment.platform 1

experiment.library_source 1

experiment.library_selection 1

  • RANDOM · 75 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Hatching · 75 ✖
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
11747 11747 ERR11608177 ERX11010308 ERS15939662 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU2 SAMEA113945412 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945412|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU2|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU2|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU2 p MU2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU2_R1.fastq.gz MU2_R2.fastq.gz fastq fastq 8373912900.0 27913043.0 E MTAB 13116:MU2 R 0:150 1:150 A:2149105370;C:2028251580;G:2055193482;T:2141168979;N:193489 150 150     2149105370 2028251580 2055193482 2141168979 193489 ERX11010308 ERS15939662 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11748 11748 ERR11608179 ERX11010310 ERS15939664 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT1 SAMEA113945414 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945414|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:WT1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:WT1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT1 p WT1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT1_R1.fastq.gz WT1_R2.fastq.gz fastq fastq 6729388500.0 22431295.0 E MTAB 13116:WT1 R 0:150 1:150 A:1730015872;C:1621295817;G:1657133586;T:1720858352;N:84873 150 150     1730015872 1621295817 1657133586 1720858352 84873 ERX11010310 ERS15939664 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11749 11749 ERR11608176 ERX11010307 ERS15939661 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU1 SAMEA113945411 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945411|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU1|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU1|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU1 p MU1 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU1_R1.fastq.gz MU1_R2.fastq.gz fastq fastq 7310352000.0 24367840.0 E MTAB 13116:MU1 R 0:150 1:150 A:1888660247;C:1748082353;G:1788562372;T:1884958596;N:88432 150 150     1888660247 1748082353 1788562372 1884958596 88432 ERX11010307 ERS15939661 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11750 11750 ERR11608178 ERX11010309 ERS15939663 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. MU3 SAMEA113945413 Shanghai Institute of Nutrition and Diseases, Chinese Academy of Sciences ENA first public:2024 07 01|External Id:SAMEA113945413|INSDC center name:Shanghai Institute of Nutrition and Diseases Chinese Academy of Sciences|INSDC last update:2023 06 27T11:19:32Z|INSDC status:public|Submitter Id:E MTAB 13116:MU3|age:48|broker name:ArrayExpress|cell type:erythrocyte|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|disease:normal|genotype:kdm4b / |genotype:wild type genotype|geographic location country and/or sea:not collected|immunophenotype:gata1 positive|individual:mixed pool of 200 individuals|isolate:not applicable|organism part:embryo|sample name:E MTAB 13116:MU3|scientific name:Danio rerio|sex:mixed|strain:Tubingen                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:MU3 p MU3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 MU3_R1.fastq.gz MU3_R2.fastq.gz fastq fastq 8826207900.0 29420693.0 E MTAB 13116:MU3 R 0:150 1:150 A:2298326835;C:2100185951;G:2130807919;T:2296678033;N:209162 150 150     2298326835 2100185951 2130807919 2296678033 209162 ERX11010309 ERS15939663 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11751 11751 ERR11608180 ERX11010311 ERS15939665 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT2 E MTAB 13116:WT2   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT2 p WT2 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT2_R1.fastq.gz WT2_R2.fastq.gz fastq fastq 8368621500.0 27895405.0 E MTAB 13116:WT2 R 0:150 1:150 A:2126734187;C:2050458346;G:2078646608;T:2112586140;N:196219 150 150     2126734187 2050458346 2078646608 2112586140 196219 ERX11010311 ERS15939665 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
11752 11752 ERR11608181 ERX11010312 ERS15939666 ERP148707 PRJEB63561 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E-MTAB-13116 Transcriptome Analysis Transcriptomic differences of gata1+ erythrocytes between the kdm4b / mutants and the WT embryos at 48 hpf were analyzed by RNA sequencing. ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01   Protocols: The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system. WT3 E MTAB 13116:WT3   strain:Tubingen|disease:normal|individual:mixed pool of 200 individuals|organism:Danio rerio|organism:Danio rerio|collection date:not collected|sex:mixed|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|developmental stage:embryo stage|genotype:wild type genotype|isolate:not applicable|immunophenotype:gata1 positive|cell type:erythrocyte|age:48|geographic location country and/or sea:not collected|ENA LAST UPDATE:2023 06 27                 RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors E MTAB 13116:WT3 p WT3 p RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors The 48 hpf gata1+ erythrocytes were sorted FACSAria BD Bioscience CA USA Two independent groups of RNA from wt and kdm4b / erythrocytes were extracted using TRIzol® Reagent Life Technologies each group contains three biological repeats. post adenylation of three prime ends of double strand cDNA fragments Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then PCR was performed with Phusion High Fidelity DNA polymerase. At last PCR products were purified and the library quality was assessed on the Agilent Bioanalyzer 2100 system.   RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina NovaSeq 6000   ERP148707 Illumina NovaSeq 6000 paired end sequencing; RNA seq of Danio rerio wild type and kdm4b knockout mutant gata1+ erythroid progenitors and precursors ENA FIRST PUBLIC:2024 07 01|ENA LAST UPDATE:2024 07 01 WT3_R1.fastq.gz WT3_R2.fastq.gz fastq fastq 8718445500.0 29061485.0 E MTAB 13116:WT3 R 0:150 1:150 A:2244668655;C:2103611849;G:2135345835;T:2234609621;N:209540 150 150     2244668655 2103611849 2135345835 2234609621 209540 ERX11010312 ERS15939666 ERA24542523 European Bioinformatics Institute|European Nucleotide Archive European Bioinformatics Institute|European Nucleotide Archive                       B B biological fallback assumption illumina novaseq_era 3prime random_priming unknown bulk unknown unknown   United Kingdom 2023-06-27 Hatching Embryo Whole Organism All anatomical structures
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
32370 32370 SRR29180530 SRX24700714 SRS21428245 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         DES   isolate:exposure to DES|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to DES|BioSampleModel:Model organism or animal                 RNA seq of DES treated DES DES Sequencing the transcriptomes of zebrafish embryos of DES treated     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 4000   SRP509851     DES_TAAGGC_L001_R1_001.fastq.gz DES_TAAGGC_L001_R2_001.fastq.gz fastq fastq 9169560000.0 30565200.0 DES TAAGGC L001 R1 001.fastq.gz 0:150 1:150 A:2545096687;C:2037322055;G:2024787099;T:2562124529;N:229630 150 150     2545096687 2037322055 2024787099 2562124529 229630 SRX24700714 SRS21428245 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
32371 32371 SRR29180531 SRX24700713 SRS21428246 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         IOX   isolate:exposure to IOX|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:exposure to IOX|BioSampleModel:Model organism or animal                 RNA seq of IOX treated IOX IOX Sequencing the transcriptomes of zebrafish embryos of IOX treated     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     IOX_CGTACT_L001_R1_001.fastq.gz IOX_CGTACT_L001_R2_001.fastq.gz fastq fastq 9547157100.0 31823857.0 IOX CGTACT L001 R1 001.fastq.gz 0:150 1:150 A:2631030736;C:2146265744;G:2124421595;T:2645201596;N:237429 150 150     2631030736 2146265744 2124421595 2645201596 237429 SRX24700713 SRS21428246 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
32372 32372 SRR29180532 SRX24700712 SRS21428244 SRP509851 PRJNA1116337 Ioxynil and diethylstilbestrol disrupt vascular and heart development in zebrafish PRJNA1116337 Other Endocrine disruption is one of the consequences of industrialization and chemicals released into theenvironment have a profound impact on organisms. Waterborne micromolar concentrations of ioxynil IOX and diethylstilbestrol DES in fish affect the development of the heart vasculature and thyroid gland.         CTR   isolate:control|age:48 hpf|dev stage:embryos|collection date:2018 06|geo loc name:Portugal|sex:pooled male and female|tissue:embryos|treatment:control|BioSampleModel:Model organism or animal                 RNA seq of CTR treated CTR CTR Sequencing the transcriptomes of zebrafish embryos of control     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP509851     CTR_AGGCAG_L001_R1_001.fastq.gz CTR_AGGCAG_L001_R2_001.fastq.gz fastq fastq 9602954100.0 32009847.0 CTR AGGCAG L001 R1 001.fastq.gz 0:150 1:150 A:2637866848;C:2169057233;G:2152906664;T:2642882530;N:240825 150 150     2637866848 2169057233 2152906664 2642882530 240825 SRX24700712 SRS21428244 SRA1878028 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-05-25 Hatching Embryo Embryo Imprecise All anatomical structures
39828 39828 SRR2437828 SRX1321832 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.normoxia.3.10329X16 48hpf.normoxia.3.10329X16 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X16_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 985942500.0 19718850.0 48hpf.normoxia.3.10329X16 0:50 A:251856100;C:223081125;G:216430606;T:294554748;N:19921 50       251856100 223081125 216430606 294554748 19921 SRX1321832 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94791   0.26704   0.68708   0.54445   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39830 39830 SRR2433795 SRX1321830 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.3. 60hpf.normoxia.3. We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X8_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1112799950.0 22255999.0 60hpf.normoxia.3. 0:50 A:294304558;C:248234752;G:238088577;T:332109252;N:62811 50       294304558 248234752 238088577 332109252 62811 SRX1321830 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94922   0.34314   0.67838   0.51455   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39832 39832 SRR2417497 SRX1321828 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.3.10329X25 48hpf.hypoxia.3.10329X25 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X25_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1234710500.0 24694210.0 48hpf.hypoxia.3.10329X25 0:50 A:309392529;C:284311489;G:275471070;T:365515358;N:20054 50       309392529 284311489 275471070 365515358 20054 SRX1321828 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94675   0.25877   0.71453   0.5239   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-16 Hatching Embryo Brain Nervous System
39833 39833 SRR2417496 SRX1321827 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.2.10329X28 60hpf.normoxia.2.10329X28 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X28_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1015786750.0 20315735.0 60hpf.normoxia.2.10329X28 0:50 A:259102784;C:230364456;G:226008843;T:300294199;N:16468 50       259102784 230364456 226008843 300294199 16468 SRX1321827 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95197   0.30503   0.68333   0.52243   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-16 Hatching Embryo Brain Nervous System
39837 39837 SRR2342161 SRX1321823 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.3.10329X27 60hpf.hypoxia.3.10329X27 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X27_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1073269500.0 21465390.0 60hpf.hypoxia.3.10329X27 0:50 A:280500644;C:237758835;G:234061287;T:320931292;N:17442 50       280500644 237758835 234061287 320931292 17442 SRX1321823 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94774   0.36354   0.70065   0.51075   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39838 39838 SRR2341509 SRX1321822 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.normoxia.210329X26 48hpf.normoxia.210329X26 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X26_130822_SN141_0719_AD2CK5ACXX_8.txt.gz fastq 1075868850.0 21517377.0 48hpf.normoxia.210329X26 0:50 A:271795722;C:246789566;G:240496674;T:316769688;N:17200 50       271795722 246789566 240496674 316769688 17200 SRX1321822 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94644   0.26805   0.68745   0.53833   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39844 39844 SRR2241311 SRX1321816 SRS1109644 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following normoxia   60hpf Normoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf Normoxia 60hpf.normoxia.1.10329X18 60hpf.normoxia.1.10329X18 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X18_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1118115050.0 22362301.0 60hpf.normoxia.1.10329X18 0:50 A:287072563;C:255244675;G:248573701;T:327203388;N:20723 50       287072563 255244675 248573701 327203388 20723 SRX1321816 SRS1109644 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.93238   0.30064   0.68574   0.51934   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39845 39845 SRR2240748 SRX1321815 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.2.10329X17 60hpf.hypoxia.2.10329X17 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X17_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1074686900.0 21493738.0 60hpf.hypoxia.2.10329X17 0:50 A:276432361;C:244039609;G:234638386;T:319556004;N:20540 50       276432361 244039609 234638386 319556004 20540 SRX1321815 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.9502   0.3077   0.6899   0.50645   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-03 Hatching Embryo Brain Nervous System
39846 39846 SRR2239869 SRX1321814 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.2.10329X15 48hpf.hypoxia.2.10329X15 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X15_130822_SN141_0719_AD2CK5ACXX_6.txt.gz fastq 1111913550.0 22238271.0 48hpf.hypoxia.2.10329X15 0:50 A:288023952;C:248947169;G:243195362;T:331723738;N:23329 50       288023952 248947169 243195362 331723738 23329 SRX1321814 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.93753   0.34521   0.70246   0.51535   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39852 39852 SRR2225888 SRX1321808 SRS1109648 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 60hpf following hypoxia   60hpf hypoxia   strain:TU|age:60hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 60hpf hypoxia 60hpf.hypoxia.1.10329X7 60hpf.hypoxia.1.10329X7 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X7_130822_SN141_0719_AD2CK5ACXX_5.txt.gz fastq 1102232350.0 22044647.0 60hpf.hypoxia.1.10329X7 0:50 A:288570352;C:247978180;G:238128703;T:327492563;N:62552 50       288570352 247978180 238128703 327492563 62552 SRX1321808 SRS1109648 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94824   0.31808   0.69244   0.51505   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-10-10 Hatching Embryo Brain Nervous System
39853 39853 SRR2225789 SRX1321807 SRS1109646 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following hypoxia   48hpf hypoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:hypoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf hypoxia 48hpf.hypoxia.1.10329X6 48hpf.hypoxia.1.10329X6 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X6_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1250042950.0 25000859.0 48hpf.hypoxia.1.10329X6 0:50 A:312511165;C:283310381;G:277279378;T:376891744;N:50282 50       312511165 283310381 277279378 376891744 50282 SRX1321807 SRS1109646 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.94959   0.28331   0.68757   0.53976   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Hatching Embryo Brain Nervous System
39856 39856 SRR2222835 SRX1321804 SRS1109643 SRP062493 PRJNA293106 Danio rerio Raw sequence reads PRJNA293106 Metagenomics Zebrafish Hypoxia RNAseq     RNAseq at 48hpf following normoxia   48hpf normoxia   strain:TU|age:48hpf|sex:not determined|tissue:brain|treatment:normoxia|BioSampleModel:Model organism or animal                 Zebrafish Embryonic Development Hypoxia Versus Normoxia RNAseq: Sample 48hpf normoxia 48hpf.1.10329X1 48hpf.1.10329X1 We collected whole RNA from zebrafish at five different embryonic developmental stages with experimental triplicates for each stage time point and experimental condition. For hypoxia we placed developing embryos in pre conditioned media in a sealed plexiglass chamber set to a reduced oxygen concentration for 12 hour periods. Immediately following hypoxia or normoxia embryos were sacrificed and RNA collected. We used 1% pO2 for ages up to 48 hpf and 4% pO2 for older ages. At the time point for collection embryos were dissected and only head tissue was used for subsequent RNA preparation. RNA was prepared with a miRNeasy kit Qiagen. Quality of total RNAs was checked using a NanoDrop 2000 Spectrometer and an Agilent 2100 Bioanalyzer. The sequencing libraries were created using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit with Ribo Zero. These libraries were sequenced on an Illumina HiSeq2000 sequencer for 50 cycles ie. 50 nucleotides single end stranded using Illumina’s version 3 chemistry. 6 samples were multiplexed together in each lane of the sequencer providing an average yield of 25.1 million reads per sample. The base calling was performed using Illumina’s CASAVA version 1.8.2 software.     RNA-Seq TRANSCRIPTOMIC RANDOM SINGLE ILLUMINA Illumina HiSeq 2000 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>50</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP062493     10329X1_130822_SN141_0719_AD2CK5ACXX_4.txt.gz fastq 1215136450.0 24302729.0 48hpf.1.10329X1 0:50 A:291802893;C:276442849;G:277217342;T:369624915;N:48451 50       291802893 276442849 277217342 369624915 48451 SRX1321804 SRS1109643 SRA289450 University of Utah|Bonkowsky University of Utah 1 0.95575   0.23021   0.72679   0.60296   50   B   usable mapping rate illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   United States 2015-09-01 Hatching Embryo Brain Nervous System
49738 49738 SRR8009939 SRX4840767 SRS3905926 SRP165180 PRJNA495704 Danio rerio strain:Tubingen Transcriptome or Gene expression PRJNA495704 Other Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.     Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. Danio rerio SMAR1 Morpholino mediated knockdown SMAR1 Morpholino   strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal                 RNA Seq of SMAR1 Morpholino injected Danio rerio Embryo TB1 MO 1 TB1 MO 1 Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 500   SRP165180         4848491136.0 31897968.0 TB1 MO 1 R2.fastq.gz 0:76 1:76 A:1279455755;C:1177863867;G:1126629683;T:1263248208;N:1293623 76 76     1279455755 1177863867 1126629683 1263248208 1293623 SRX4840767 SRS3905926 SRA792799 Indian Institute of Chemical Biology|Chromatin and Disease Biology Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad 2 0.94763 0.94494 0.08466 0.0847 0.68477 0.68941 0.45531 0.46264 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   India 2018-10-11 Hatching Embryo Whole Organism All anatomical structures
49739 49739 SRR8009940 SRX4840766 SRS3905926 SRP165180 PRJNA495704 Danio rerio strain:Tubingen Transcriptome or Gene expression PRJNA495704 Other Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.     Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. Danio rerio SMAR1 Morpholino mediated knockdown SMAR1 Morpholino   strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal                 RNA Seq of SMAR1 Morpholino injected Danio rerio Embryo TB1 MO 2 TB1 MO 2 Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 500   SRP165180         5229981040.0 34407770.0 TB1 MO 2 R2.fastq.gz 0:76 1:76 A:1375946341;C:1255628851;G:1212656512;T:1382649755;N:3099581 76 76     1375946341 1255628851 1212656512 1382649755 3099581 SRX4840766 SRS3905926 SRA792799 Indian Institute of Chemical Biology|Chromatin and Disease Biology Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad 2 0.95547 0.95355 0.08995 0.08948 0.6799 0.68365 0.46004 0.46022 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   India 2018-10-11 Hatching Embryo Whole Organism All anatomical structures
49740 49740 SRR8009941 SRX4840765 SRS3905926 SRP165180 PRJNA495704 Danio rerio strain:Tubingen Transcriptome or Gene expression PRJNA495704 Other Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.     Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. Danio rerio SMAR1 Morpholino mediated knockdown SMAR1 Morpholino   strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal                 RNA Seq of Control Morpholino injected Danio rerio Embryo CTRL MO 1 CTRL MO 1 Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 500   SRP165180         5396333184.0 35502192.0 CTRL MO 1 R2.fastq.gz 0:76 1:76 A:1423972325;C:1290764003;G:1246450472;T:1431965693;N:3180691 76 76     1423972325 1290764003 1246450472 1431965693 3180691 SRX4840765 SRS3905926 SRA792799 Indian Institute of Chemical Biology|Chromatin and Disease Biology Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad 2 0.95835 0.95512 0.09447 0.09425 0.68038 0.68416 0.4619 0.45317 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   India 2018-10-11 Hatching Embryo Whole Organism All anatomical structures
49741 49741 SRR8009942 SRX4840764 SRS3905926 SRP165180 PRJNA495704 Danio rerio strain:Tubingen Transcriptome or Gene expression PRJNA495704 Other Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos.     Scaffold Matrix Attachment Region 1 SMAR1 is a characterised nuclear matrix binding protein. It is thought to be a mammalian protein that plays role in a various nuclear functions. In the present study we have identified and characterised SMAR1 homologue in zebrafish zSMAR1 of 2.43 Kb length consisting of 13 exons that encodes a 508 amino acid long protein. zSMAR1 shares 66% homology to mouse SMAR1. Morpholino antisense oligonucleotide MO mediated knock down of zSMAR1 in fish embryos led to embryonic malformations smaller head size pericardial edema and a linear heart tube phenotype indicating its role in fish embryogenesis. The present RNA Seq data is generated on Illumina NextSeq 500 platform yielding 75 nucleotide long reads in paired end format. The samples used for sequencing are Control MO injected and MO targeting zSMAR1 injected zebrafish embryos. Danio rerio SMAR1 Morpholino mediated knockdown SMAR1 Morpholino   strain:Tubingen|age:48 hpf|dev stage:Long pec 48hpf|sex:not applicable|tissue:Whole embryo|biomaterial provider:Dr. Mahendra Sonawane TIFR|collected by:Sonal Patel NCCS|treatment:SMAR1 Morpholino|BioSampleModel:Model organism or animal                 RNA Seq of Control Morpholino injected Danio rerio Embryo CTRL M0 2 CTRL M0 2 Poly A Based Selection followed by Illumina NextSeq 500 sequencing yielded 75nt paired end reads     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 500   SRP165180         4661867664.0 30670182.0 CTRL MO 2 R1.fastq.gz 0:76 1:76 A:1224151482;C:1123655254;G:1082094210;T:1229195581;N:2771137 76 76     1224151482 1123655254 1082094210 1229195581 2771137 SRX4840764 SRS3905926 SRA792799 Indian Institute of Chemical Biology|Chromatin and Disease Biology Indian Institute of Chemical Biology Sandor Life Sciences Pvt. Ltd., Hyderabad 2 0.95816 0.95561 0.08583 0.08611 0.67829 0.68345 0.46037 0.45464 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   India 2018-10-11 Hatching Embryo Whole Organism All anatomical structures
51269 51269 SRR8663334 SRX5460031 SRS4433921 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 48hpf rep2 GSM3638675   source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish ZF 48hpf rep2 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish GSM3638675 GSM3638675: ZF 48hpf rep2; Danio rerio; Bisulfite Seq GSM3638675   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638675 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         21257043600.0 70856812.0 GSM3638675 r1 0:150 1:150 A:7462169931;C:3151216767;G:3428144480;T:7214024902;N:1487520 150 150     7462169931 3151216767 3428144480 7214024902 1487520 SRX5460031 SRS4433921 SRA855736 GEO Sun Yat-sen University 2 0.00062 0.00055 0.00017 0.00013 0.99949 0.99945 0.67901 0.75362 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Hatching Embryo Embryo Imprecise All anatomical structures
51270 51270 SRR8663333 SRX5460030 SRS4433920 SRP187415 PRJNA525392 Whole transcriptome bisufilte sequencing for multiple species [Zebrafish] GSE127779 Other We applied a robust experimental and computational framework to identify mRNA m5C sites with high specificity in multiple species. Overall design: RNA BS seq of mRNA for multiple species. parent bioproject:PRJNA525389 pubmed:35513466   ZF 48hpf rep1 GSM3638674   source name:embryo|tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish ZF 48hpf rep1 Basecalls performed using illumina bcl2fastq 2.17. Adapters were trimmed with cutadapt. Adapter trimmed reads were quality trimmed with Trimmomatic. Clean reads were firstly mapped to the genome and then transcriptome with hisat2 2.10 Pileup was performed using samtools API pysam. Customized scripts were used to call m5C sites from samples Genome build: Zv9.78 Supplementary files format and content: CSV files recording the coverage m5C level P value for m5C sites embryo   For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer’s protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. Embryos were reared at 28.5 °C and all experiments and observations were performed as close to this temperature as possible. tissue:embryo|developmental stage:48 hpf|strain:wild type AB fish GSM3638674 GSM3638674: ZF 48hpf rep1; Danio rerio; Bisulfite Seq GSM3638674   1 For the embryonic stages 200 embryos were collected and for the larval stage 150 larvae were collected. Total RNA was isolated with TRIzol reagent and Direct zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads Vazyme. 100ng 1μg of polyadenylated RNA was converted using the EZ RNA methylation kit Zymo Research with modified high stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer NEBNext Ultra II Directional RNA Library Prep Kit NEB. The fragmented RNA was then used for library construction following the manufacturer's protocol NEBNext Ultra II Directional RNA Library Prep Kit NEB. GEO Accession:GSM3638674 Bisulfite-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP187415         20408177400.0 68027258.0 GSM3638674 r1 0:150 1:150 A:6990585654;C:3225159172;G:3562240517;T:6628764661;N:1427396 150 150     6990585654 3225159172 3562240517 6628764661 1427396 SRX5460030 SRS4433920 SRA855736 GEO Sun Yat-sen University 2 0.0009 0.00071 0.0003 0.00019 0.99928 0.99941 0.6 0.64367 150 150 T T mates < 9% mapping rate illumina hiseq_era full_length random_priming nebnext bulk unknown unknown   China 2019-03-04 Hatching Embryo Embryo Imprecise All anatomical structures
53387 53387 SRR9849850 SRX6604478 SRS5169417 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         64h   cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 64h 2 64h 2 64h 2 circRNA sequence using embryo from zebrafish 64 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     64h-1_Clean_1.fq.gz 64h-1_Clean_2.fq.gz fastq fastq 12070643714.0 40313092.0 64h 1 Clean 1.fq.gz 0:149.71 1:149.71 A:3237260307;C:2738447871;G:2833701504;T:3260078610;N:1155422 149 149     3237260307 2738447871 2833701504 3260078610 1155422 SRX6604478 SRS5169417 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.83609 0.83872 0.41826 0.41667 0.77557 0.78397 0.47577 0.47371 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53388 53388 SRR9849851 SRX6604477 SRS5169416 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         56h   cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 56h 2 56h 2 56h 2 circRNA sequence using embryo from zebrafish 56 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     56h-1_Clean_1.fq.gz 56h-1_Clean_2.fq.gz fastq fastq 12652509916.0 42236972.0 56h 1 Clean 1.fq.gz 0:149.78 1:149.78 A:3143250045;C:3111652116;G:3204244162;T:3192159623;N:1203970 149 149     3143250045 3111652116 3204244162 3192159623 1203970 SRX6604477 SRS5169416 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.75422 0.75589 0.33145 0.32138 0.8242 0.82911 0.44098 0.47205 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53389 53389 SRR9849852 SRX6604476 SRS5169417 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         64h   cultivar:Danio rerio|age:64hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 64h 1 64h 1 64h 1 circRNA sequence using embryo from zebrafish 64 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-438_L4_7008.R1.clean.fastq.gz BN2-438_L4_7008.R2.clean.fastq.gz fastq fastq 10065278400.0 33550928.0 BN2 438 L4 7008.R1.clean.fastq.gz 0:150 1:150 A:1866703079;C:2946459459;G:3062616963;T:2188863630;N:635269 150 150     1866703079 2946459459 3062616963 2188863630 635269 SRX6604476 SRS5169417 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.9213 0.9133 0.81853 0.81548 0.96639 0.96741 0.46951 0.49212 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
53391 53391 SRR9849854 SRX6604474 SRS5169416 SRP216580 PRJNA556992 Global identification of circular RNAs during zebrafish embryogenesis PRJNA556992 Other Fertilization and embryo development guarantee the activation of totipotent zygote and tissues formation. Over past few yrs thousands of circRNAs have been identified in various animals representing a ubiquitous set of non coding RNA and conserved mechanism as essential biological functions. We sequenced RNA time series of stages with RNase R treated approach during zebrafish development in the present.         56h   cultivar:Danio rerio|age:56hpf stage:hatching|sex:not determined|tissue:not applicable|BioSampleModel:Model organism or animal                 circRNA 56h 1 56h 1 56h 1 circRNA sequence using embryo from zebrafish 56 hpf     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP216580     BN2-437_L4_7007.R1.clean.fastq.gz BN2-437_L4_7007.R2.clean.fastq.gz fastq fastq 7808518800.0 26028396.0 BN2 437 L4 7007.R1.clean.fastq.gz 0:150 1:150 A:1446244174;C:2292471599;G:2377378733;T:1691933018;N:491276 150 150     1446244174 2292471599 2377378733 1691933018 491276 SRX6604474 SRS5169416 SRA927972 Guangxi Academy of Fishery Sciences|Guangxi Academy of Fishery Sciences Guangxi Academy of Fishery Sciences 2 0.90958 0.89969 0.83016 0.82404 0.9641 0.96558 0.44242 0.44176 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2019-07-27 Hatching Embryo Embryo Imprecise All anatomical structures
55843 55843 SRR10862985 SRX7533084 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                 totalRNA of Zebrafish: PGCs 2dpf wt PGCs 2dpf rep3 totalRNA wt PGCs 2dpf rep3 totalRNA NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550   SRP241074     03072018-wt_PGCs_2dpf_rep3_totalRNA.R1.fastq.gz 03072018-wt_PGCs_2dpf_rep3_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep3_totalRNA.R1.fastq.gz 14022018-wt_PGCs_2dpf_rep3_totalRNA.R2.fastq.gz fastq fastq fastq fastq 3149016822.0 21605375.0 03072018 wt PGCs 2dpf rep3 totalRNA.R1.fastq.gz 0:72.88 1:72.88 A:882764631;C:692736186;G:686376514;T:886384367;N:755124 72 72     882764631 692736186 686376514 886384367 755124 SRX7533084 SRS5972252 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.86749 0.86961 0.31266 0.31842 0.66807 0.67359 0.63363 0.63454 75 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55844 55844 SRR10862986 SRX7533083 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                 totalRNA of Zebrafish: PGCs 2dpf wt PGCs 2dpf rep2 totalRNA wt PGCs 2dpf rep2 totalRNA NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550   SRP241074     14022018-wt_PGCs_2dpf_rep2_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep2_totalRNA.R1.fastq.gz 09072018-wt_PGCs_2dpf_rep2_totalRNA.R2.fastq.gz 09072018-wt_PGCs_2dpf_rep2_totalRNA.R1.fastq.gz fastq fastq fastq fastq 3023614944.0 20997326.0 09072018 wt PGCs 2dpf rep2 totalRNA.R1.fastq.gz 0:72 1:72 A:856012866;C:645772980;G:664213827;T:856875833;N:739438 72 72     856012866 645772980 664213827 856875833 739438 SRX7533083 SRS5972244 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.89654 0.88678 0.30038 0.29916 0.66539 0.67322 0.65371 0.65661 72 72 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55845 55845 SRR10862987 SRX7533082 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                 totalRNA of Zebrafish: PGCs 2dpf wt PGCs 2dpf rep1 totalRNA wt PGCs 2dpf rep1 totalRNA NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550   SRP241074     14022018-wt_PGCs_2dpf_rep1_totalRNA.R2.fastq.gz 14022018-wt_PGCs_2dpf_rep1_totalRNA.R1.fastq.gz 03072018-wt_PGCs_2dpf_rep1_totalRNA.R2.fastq.gz 03072018-wt_PGCs_2dpf_rep1_totalRNA.R1.fastq.gz fastq fastq fastq fastq 3143598780.0 21555803.0 03072018 wt PGCs 2dpf rep1 totalRNA.R1.fastq.gz 0:72.92 1:72.92 A:889549293;C:680890464;G:675921445;T:896506040;N:731538 72 72     889549293 680890464 675921445 896506040 731538 SRX7533082 SRS5972269 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.87081 0.87619 0.35764 0.36603 0.69112 0.69534 0.61958 0.50175 75 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55856 55856 SRR10862997 SRX7533071 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                 totalRNA of Zebrafish: Fish 2dpf wt Fish 2dpf rep2 totalRNA wt Fish 2dpf rep2 totalRNA NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550   SRP241074     14022018-wt_Fish_2dpf_rep2_totalRNA.R1.fastq.gz 14022018-wt_Fish_2dpf_rep2_totalRNA.R2.fastq.gz fastq fastq 2393393904.0 16620791.0 14022018 wt Fish 2dpf rep2 totalRNA.R1.fastq.gz 0:72 1:72 A:686360274;C:500344029;G:513640853;T:692249479;N:799269 72 72     686360274 500344029 513640853 692249479 799269 SRX7533071 SRS5972259 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.89258 0.88294 0.37278 0.37257 0.72196 0.72835 0.47632 0.45833 72 72 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
55857 55857 SRR10862998 SRX7533070 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                 totalRNA of Zebrafish: Fish 2dpf wt Fish 2dpf rep1 totalRNA wt Fish 2dpf rep1 totalRNA NGS library prep was performed with NuGen Ovation SoLo RNA Seq System following NuGen`s standard protocol M01406v2. Libraries were prepared with a starting amount of 1 ng and amplified in 14 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer Agilent technologies and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer Life technologies. Samples were pooled in equimolar ratio and sequenced PE for 2x 75 cycles plus 16 cycles for the index read. Small RNA sequencing     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA NextSeq 550   SRP241074     14022018-wt_Fish_2dpf_rep1_totalRNA.R1.fastq.gz 14022018-wt_Fish_2dpf_rep1_totalRNA.R2.fastq.gz fastq fastq 2385260496.0 16564309.0 14022018 wt Fish 2dpf rep1 totalRNA.R1.fastq.gz 0:72 1:72 A:700046007;C:483087371;G:497985107;T:703351178;N:790833 72 72     700046007 483087371 497985107 703351178 790833 SRX7533070 SRS5972258 SRA1023320 Rene Ketting group|Ketting Lab Rene Ketting group 2 0.75478 0.74465 0.32465 0.3237 0.74237 0.7511 0.59403 0.59404 72 72 B B biological fallback assumption illumina nextseq unknown random_priming unknown bulk unknown unknown   Germany 2020-01-10 Hatching Embryo Whole Organism All anatomical structures
57192 57192 SRR11267487 SRX7874167 SRS6282472 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 4   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 2dpf wild type replicate 4 2D wt 4 2D wt 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W4_RRA127644-V_2.fq.gz s-2D-W4_RRA127644-V_1.fq.gz fastq fastq 8446821000.0 28156070.0 s 2D W4 RRA127644 V 1.fq.gz 0:150 1:150 A:2097825166;C:2140144849;G:2138243343;T:2070561208;N:46434 150 150     2097825166 2140144849 2138243343 2070561208 46434 SRX7874167 SRS6282472 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96179 0.9619 0.03544 0.03525 0.73484 0.73476 0.46149 0.46378 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57193 57193 SRR11267488 SRX7874166 SRS6282471 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 3   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 2dpf wild type replicate 3 2D wt 3 2D wt 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W3_RRA127643-V_2.fq.gz s-2D-W3_RRA127643-V_1.fq.gz fastq fastq 7574668800.0 25248896.0 s 2D W3 RRA127643 V 1.fq.gz 0:150 1:150 A:1965967840;C:1838044502;G:1837157311;T:1933458605;N:40542 150 150     1965967840 1838044502 1837157311 1933458605 40542 SRX7874166 SRS6282471 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.94714 0.94809 0.06053 0.06005 0.70601 0.7066 0.44616 0.4478 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57194 57194 SRR11267489 SRX7874165 SRS6282470 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 2   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 2dpf wild type replicate 2 2D wt 2 2D wt 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W2_RRA127642-V_1.fq.gz s-2D-W2_RRA127642-V_2.fq.gz fastq fastq 6972507000.0 23241690.0 s 2D W2 RRA127642 V 1.fq.gz 0:150 1:150 A:1813207623;C:1690998145;G:1687754190;T:1780508001;N:39041 150 150     1813207623 1690998145 1687754190 1780508001 39041 SRX7874165 SRS6282470 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.94999 0.95119 0.05951 0.0596 0.7077 0.70778 0.45098 0.44895 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57195 57195 SRR11267490 SRX7874164 SRS6282468 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 1   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 2dpf wild type replicate 1 2D wt 1 2D wt 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W1_RRA127641-V_1.fq.gz s-2D-W1_RRA127641-V_2.fq.gz fastq fastq 7527697800.0 25092326.0 s 2D W1 RRA127641 V 1.fq.gz 0:150 1:150 A:1939383301;C:1841967572;G:1840198678;T:1906107300;N:40949 150 150     1939383301 1841967572 1840198678 1906107300 40949 SRX7874164 SRS6282468 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.93028 0.93025 0.05585 0.05522 0.71163 0.71281 0.45427 0.45339 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57196 57196 SRR11267491 SRX7874163 SRS6282469 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 6   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 2dpf mutant replicate 6 2D mut 6 2D mut 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU6_RRA127640-V_1.fq.gz s-2D-MU6_RRA127640-V_2.fq.gz fastq fastq 7468400400.0 24894668.0 s 2D MU6 RRA127640 V 1.fq.gz 0:150 1:150 A:1831861636;C:1917846110;G:1910771652;T:1807881608;N:39394 150 150     1831861636 1917846110 1910771652 1807881608 39394 SRX7874163 SRS6282469 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96824 0.96912 0.02823 0.02789 0.76116 0.76086 0.46225 0.46104 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57205 57205 SRR11267500 SRX7874154 SRS6282459 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 5   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 2dpf mutant replicate 5 2D mut 5 2D mut 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU5_RRA127639-V_1.fq.gz s-2D-MU5_RRA127639-V_2.fq.gz fastq fastq 7610707500.0 25369025.0 s 2D MU5 RRA127639 V 1.fq.gz 0:150 1:150 A:1916314949;C:1902998959;G:1903573416;T:1887778592;N:41584 150 150     1916314949 1902998959 1903573416 1887778592 41584 SRX7874154 SRS6282459 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95723 0.95704 0.04362 0.04378 0.7231 0.72196 0.45408 0.45325 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57216 57216 SRR11267511 SRX7874143 SRS6282448 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 4   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 2dpf mutant replicate 4 2D mut 4 2D mut 4 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU4_RRA127638-V_2.fq.gz s-2D-MU4_RRA127638-V_1.fq.gz fastq fastq 7971688200.0 26572294.0 s 2D MU4 RRA127638 V 1.fq.gz 0:150 1:150 A:1975296205;C:2025572304;G:2026332631;T:1944443854;N:43206 150 150     1975296205 2025572304 2026332631 1944443854 43206 SRX7874143 SRS6282448 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96253 0.96256 0.03284 0.03254 0.75057 0.75079 0.45472 0.45579 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57227 57227 SRR11267522 SRX7874132 SRS6282437 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 3   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 2dpf mutant replicate 3 2D mut 3 2D mut 3 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU3_RRA127637-V_1.fq.gz s-2D-MU3_RRA127637-V_2.fq.gz fastq fastq 8159715900.0 27199053.0 s 2D MU3 RRA127637 V 1.fq.gz 0:150 1:150 A:2021631175;C:2074621188;G:2072837540;T:1990581511;N:44486 150 150     2021631175 2074621188 2072837540 1990581511 44486 SRX7874132 SRS6282437 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96275 0.9634 0.02909 0.02886 0.75035 0.75035 0.46995 0.46205 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57236 57236 SRR11267531 SRX7874123 SRS6282428 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 6   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 2dpf wild type replicate 6 2D wt 6 2D wt 6 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W6_RRA127646-V_1.fq.gz s-2D-W6_RRA127646-V_2.fq.gz fastq fastq 7672945500.0 25576485.0 s 2D W6 RRA127646 V 1.fq.gz 0:150 1:150 A:1904102253;C:1945024582;G:1945915237;T:1877861524;N:41904 150 150     1904102253 1945024582 1945915237 1877861524 41904 SRX7874123 SRS6282428 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96213 0.96229 0.02936 0.0295 0.74418 0.74428 0.46242 0.46223 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57237 57237 SRR11267532 SRX7874122 SRS6282426 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D wt 5   strain:Abtu|ecotype:wild type|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 2dpf wild type replicate 5 2D wt 5 2D wt 5 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-W5_RRA127645-V_1.fq.gz s-2D-W5_RRA127645-V_2.fq.gz fastq fastq 6602868900.0 22009563.0 s 2D W5 RRA127645 V 1.fq.gz 0:150 1:150 A:1688419207;C:1625631997;G:1626136783;T:1662643961;N:36952 150 150     1688419207 1625631997 1626136783 1662643961 36952 SRX7874122 SRS6282426 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.956 0.95646 0.04794 0.04766 0.72226 0.72316 0.45044 0.44816 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57238 57238 SRR11267533 SRX7874121 SRS6282427 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 2   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 2dpf mutant replicate 2 2D mut 2 2D mut 2 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU2_RRA127636-V_1.fq.gz s-2D-MU2_RRA127636-V_2.fq.gz fastq fastq 7639000500.0 25463335.0 s 2D MU2 RRA127636 V 1.fq.gz 0:150 1:150 A:1914314950;C:1916936042;G:1919603914;T:1888104180;N:41414 150 150     1914314950 1916936042 1919603914 1888104180 41414 SRX7874121 SRS6282427 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.95818 0.95815 0.03971 0.03906 0.72247 0.72236 0.44884 0.45872 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
57239 57239 SRR11267534 SRX7874120 SRS6282425 SRP252014 PRJNA611476 RNAseq between mutant and wild type zebrafish at different developmental stages PRJNA611476 Other           2D mut 1   strain:Abtu|ecotype:mutant|dev stage:2dpf|sex:missing|tissue:embryos|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 2dpf mutant replicate 1 2D mut 1 2D mut 1 common method     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2000   SRP252014     s-2D-MU1_RRA127635-V_1.fq.gz s-2D-MU1_RRA127635-V_2.fq.gz fastq fastq 7955196900.0 26517323.0 s 2D MU1 RRA127635 V 1.fq.gz 0:150 1:150 A:1980678540;C:2010190992;G:2012301601;T:1951981643;N:44124 150 150     1980678540 2010190992 2012301601 1951981643 44124 SRX7874120 SRS6282425 SRA1052323 Sun Yat-sen University|College of Life Sciences Sun Yat-sen University 2 0.96174 0.96124 0.03506 0.03487 0.73866 0.73921 0.4672 0.4643 150 150 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2020-03-09 Hatching Embryo Embryo Imprecise All anatomical structures
69475 69475 SRR18712324 SRX14812927 SRS12569570 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 60hpf WT b   strain:WT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 60 hpf larvae WT for the eMIC domain of srrm3. Eye 60hpf WT Eye 60hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_60hpf_WT_b_R1-125.fq.gz Eye_60hpf_WT_b_R2-125.fq.gz fastq fastq 15250592500.0 61002370.0 Eye 60hpf WT b R1 125.fq.gz 0:125 1:125 A:3923837289;C:3702942025;G:3742033933;T:3872922356;N:8856897 125 125     3923837289 3702942025 3742033933 3872922356 8856897 SRX14812927 SRS12569570 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97168 0.9731 0.0527 0.05258 0.69891 0.70041 0.45973 0.45381 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69476 69476 SRR18712325 SRX14812926 SRS12569569 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 60hpf MUT b   strain:srrm3 MUT|dev stage:60 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 60 hpf larvae mutated for the eMIC domain of srrm3. Eye 60hpf MUT Eye 60hpf MUT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_60hpf_MUT_b_R1-125.fq.gz Eye_60hpf_MUT_b_R2-125.fq.gz fastq fastq 14932544250.0 59730177.0 Eye 60hpf MUT b R1 125.fq.gz 0:125 1:125 A:3891825609;C:3575114135;G:3598083383;T:3858808039;N:8713084 125 125     3891825609 3575114135 3598083383 3858808039 8713084 SRX14812926 SRS12569569 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.96985 0.97098 0.06006 0.0593 0.68939 0.6926 0.46001 0.45867 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69477 69477 SRR18712326 SRX14812925 SRS12569568 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 48hpf WT b   strain:WT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 48 hpf larvae WT for the eMIC domain of srrm3. Eye 48hpf WT Eye 48hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_48hpf_WT_b_R1-125.fq.gz Eye_48hpf_WT_b_R2-125.fq.gz fastq fastq 15736041750.0 62944167.0 Eye 48hpf WT b R1 125.fq.gz 0:125 1:125 A:4076543478;C:3787178416;G:3834447099;T:4028745594;N:9127163 125 125     4076543478 3787178416 3834447099 4028745594 9127163 SRX14812925 SRS12569568 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97095 0.97209 0.05101 0.05067 0.69408 0.69767 0.47501 0.47714 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System
69478 69478 SRR18712327 SRX14812924 SRS12569567 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Eye 48hpf MUT b   strain:srrm3 MUT|dev stage:48 hpf|sex:NA|tissue:Eye|BioSampleModel:Model organism or animal                 Eyes from 48 hpf larvae mutated for the eMIC domain of srrm3. Eye 48hpf MUT Eye 48hpf MUT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Eye_48hpf_MUT_b_R1-125.fq.gz Eye_48hpf_MUT_b_R2-125.fq.gz fastq fastq 14845531750.0 59382127.0 Eye 48hpf MUT b R1 125.fq.gz 0:125 1:125 A:3879709745;C:3539390575;G:3573173326;T:3844623832;N:8634272 125 125     3879709745 3539390575 3573173326 3844623832 8634272 SRX14812924 SRS12569567 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.9684 0.97006 0.05578 0.05498 0.69183 0.69581 0.472 0.46674 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Hatching Embryo Eye Sensory System

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