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
41,DRR408245,DRX393851,DRS407176,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 3,zebrafish EN replicate 3,SAMD00529465,,sample name:zebrafish EN replicate 3|biological replicate:eneteric neurons 3|strain:TgSAGFFLF219B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529465,DRX393851,190326ENvsNC N703 5day;EntericNeuron;rep3,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529465,,,,3729799291.0,23985772.0,DRR408245,0:77.75 1:77.75,A:978752781;C:879988139;G:903976580;T:962122970;N:4958821,77,77,,,978752781,879988139,903976580,962122970,4958821,DRX393851,DRS407176,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
42,DRR408244,DRX393850,DRS407175,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 2,zebrafish EN replicate 2,SAMD00529464,,sample name:zebrafish EN replicate 2|biological replicate:eneteric neurons 2|strain:TgSAGFFLF218B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529464,DRX393850,190326ENvsNC N702 5day;EntericNeuron;rep2,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529464,,,,3315994810.0,21477755.0,DRR408244,0:77.19 1:77.20,A:873970427;C:778042505;G:798459853;T:859611841;N:5910184,77,77,,,873970427,778042505,798459853,859611841,5910184,DRX393850,DRS407175,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
43,DRR408243,DRX393849,DRS407174,DRP012042,PRJDB14275,Zebrafish EN/ENCDC RNA seq,DRP012042,Transcriptome Analysis,A project to find differential expressed genes between enteric neurons ENs and enteric neural crest derived cells ENCDCs in larval zebrafish gut. We dissected guts of transgenic line  TgSAGFFLF217B; uas:gfp for ENs and Tgsox10:cre; EF1alpha:loxP gfp loxP dsred for ENCDCs  and isolated GFP+ ENs and dsRed+ ENCDCs.  Three duplicates for each of ENs and ENCDCs are prepared. Libraries for NGS are prepared using SMART Seq V4 Ultra Low Input RNA Kit.,,,zebrafish 5 day GFP positive enteric neurons replicate 1,zebrafish EN replicate 1,SAMD00529463,,sample name:zebrafish EN replicate 1|biological replicate:eneteric neurons 1|strain:TgSAGFFLF217B; uas:gfp,,,,,,,,,NextSeq 550 paired end sequencing of SAMD00529463,DRX393849,190326ENvsNC N701 5day;EntericNeuron;rep1,1,1,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,NextSeq 550,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>160</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><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>81</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP012042,NextSeq 550 paired end sequencing of SAMD00529463,,,,2999501518.0,19455440.0,DRR408243,0:77.08 1:77.09,A:788053541;C:705895776;G:724185148;T:775760738;N:5606315,77,77,,,788053541,705895776,724185148,775760738,5606315,DRX393849,DRS407174,DRA014886,"NIBB|NIBB core research facilities, National Institute for Basic Biology",University of Hyogo,,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2024-09-22,Undetermined,Larval,Undetermined,Undetermined
9951,ERR5961093,ERX5601614,ERS6490233,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the same batch.,Uninjected2,Uninjected2,,ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 12 14|ENA LAST UPDATE:2021 12 14,,,,,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 8,,,,,,,,,,,,ERX5601614,,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,,,,,,,,,,,,,,,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9952,ERR5961092,ERX5601613,ERS6490232,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the same batch.,Uninjected1,SAMEA8805898,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 06 23|ENA last update:2021 06 23|External Id:SAMEA8805898|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 06 23T08:18:31Z|INSDC last update:2021 06 23T08:18:31Z|INSDC status:public|Submitter Id:Uninjected1|common name:zebrafish|sample name:Uninjected1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 06 23|ENA LAST UPDATE:2021 06 23,WT1_R1_001.fastq WT1_R2_001.fastq,fastq fastq,5664550800.0,18881836.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 7,0:150 1:150,A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763,150,150,,,1493322675,1337347146,1388414458,1444981758,484763,ERX5601613,ERS6490232,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95769,0.95822,0.04407,0.04391,0.69934,0.69958,0.4411,0.45319,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9953,ERR5961096,ERX5601617,ERS6490236,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected5,SAMEA8805902,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805902|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected5|common name:zebrafish|sample name:Uninjected5,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT5_R1_001.fastq.gz WT5_R2_001.fastq.gz,fastq fastq,9088444200.0,30294814.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 11,0:150 1:150,A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622,150,150,,,2404715160,2098546919,2330441921,2254532578,207622,ERX5601617,ERS6490236,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95076,0.93857,0.06296,0.06222,0.68485,0.70047,0.47429,0.48524,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9954,ERR5961095,ERX5601616,ERS6490235,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected4,SAMEA8805901,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805901|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected4|common name:zebrafish|sample name:Uninjected4,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT4_R1_001.fastq.gz WT4_R2_001.fastq.gz,fastq fastq,9222083700.0,30740279.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 10,0:150 1:150,A:2328864269;C:2117919914;G:2560286870;T:2214801519;N:211128,150,150,,,2328864269,2117919914,2560286870,2214801519,211128,ERX5601616,ERS6490235,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95124,0.92695,0.05122,0.05036,0.69118,0.70634,0.47769,0.47806,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9955,ERR5961094,ERX5601615,ERS6490234,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae uninjected controls from the an additional batch.,Uninjected3,SAMEA8805900,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805900|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Uninjected3|common name:zebrafish|sample name:Uninjected3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,WT3_R1_001.fastq.gz WT3_R2_001.fastq.gz,fastq fastq,9088444200.0,30294814.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:032 9,0:150 1:150,A:2404715160;C:2098546919;G:2330441921;T:2254532578;N:207622,150,150,,,2404715160,2098546919,2330441921,2254532578,207622,ERX5601615,ERS6490234,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95071,0.93855,0.06295,0.06183,0.68511,0.70065,0.47621,0.48573,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9956,ERR5961091,ERX5601612,ERS6490231,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme3,SAMEA8805897,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805897|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme3|common name:zebrafish|sample name:Cas9enzyme3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA3_R1_001.fastq RNA3_R2_001.fastq,fastq fastq,5814764400.0,19382548.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 6,0:150 1:150,A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867,150,150,,,1550014255,1359566801,1419514658,1485169819,498867,ERX5601612,ERS6490231,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96166,0.96182,0.04962,0.04954,0.68172,0.68144,0.45683,0.46611,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9957,ERR5961090,ERX5601611,ERS6490230,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme2,SAMEA8805896,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805896|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme2|common name:zebrafish|sample name:Cas9enzyme2,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA2_R1_001.fastq RNA2_R2_001.fastq,fastq fastq,5927606100.0,19758687.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 5,0:150 1:150,A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534,150,150,,,1579767222,1387675810,1439122138,1520529396,511534,ERX5601611,ERS6490230,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96217,0.96214,0.05174,0.05176,0.67083,0.6716,0.46772,0.47128,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9958,ERR5961089,ERX5601610,ERS6490229,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9 enzyme at the one cell stage.,Cas9enzyme1,SAMEA8805895,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805895|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9enzyme1|common name:zebrafish|sample name:Cas9enzyme1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,RNA1_R1_001.fastq RNA1_R2_001.fastq,fastq fastq,5738133000.0,19127110.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 4,0:150 1:150,A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691,150,150,,,1530616107,1342298453,1401357126,1463360623,500691,ERX5601610,ERS6490229,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95709,0.9569,0.05132,0.05149,0.68771,0.68846,0.45988,0.47329,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9959,ERR5961088,ERX5601609,ERS6490228,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA3,SAMEA8805894,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805894|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA3|common name:zebrafish|sample name:Cas9mRNA3,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,PRO3_R1_001.fastq PRO3_R2_001.fastq,fastq fastq,9635841900.0,32119473.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 3,0:150 1:150,A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911,150,150,,,2562857735,2253487693,2325345541,2493627020,523911,ERX5601609,ERS6490228,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95769,0.95696,0.05441,0.05397,0.67424,0.67407,0.46338,0.46444,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9960,ERR5961087,ERX5601608,ERS6490227,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA2,SAMEA8805893,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805893|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA2|common name:zebrafish|sample name:Cas9mRNA2,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 10 21,PRO2_R1_001.fastq PRO2_R2_001.fastq,fastq fastq,8990649900.0,29968833.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 2,0:150 1:150,A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619,150,150,,,2370044440,2140400380,2185347925,2294361536,495619,ERX5601608,ERS6490227,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95444,0.95397,0.05839,0.05842,0.67377,0.67207,0.48505,0.48043,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9961,ERR5961086,ERX5601607,ERS6490226,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNA seq data of 5dpf larvae injected with Cas9mRNA at the one cell stage.,Cas9mRNA1,SAMEA8805892,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2021 05 26|ENA last update:2021 05 26|External Id:SAMEA8805892|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2021 05 26T09:21:17Z|INSDC last update:2021 05 26T09:21:17Z|INSDC status:public|Submitter Id:Cas9mRNA1|common name:zebrafish|sample name:Cas9mRNA1,,,,,,,,,Illumina HiSeq 4000 paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 4000,,ERP123184,Illumina HiSeq 4000 paired end sequencing,ENA FIRST PUBLIC:2021 05 26|ENA LAST UPDATE:2021 05 26,PRO1_R1_001.fastq PRO1_R2_001.fastq,fastq fastq,8803789500.0,29345965.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 25 05 2021 08:56:51:031 1,0:150 1:150,A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952,150,150,,,2318913314,2090675347,2149054140,2244296747,849952,ERX5601607,ERS6490226,ERA4417635,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.954,0.9549,0.04652,0.04639,0.70806,0.71386,0.45393,0.44921,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9962,ERR4902960,ERX4769932,ERS5427208,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.,CRISPR RNAseq,SAMEA7670216,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670216|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:12Z|INSDC status:public|Submitter Id:CRISPR RNAseq8|common name:zebrafish|sample name:CRISPR RNAseq8,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,WT2_R1_001.fastq.gz WT2_R2_001.fastq.gz,fastq fastq,7020700500.0,23402335.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 8,0:150 1:150,A:1879937256;C:1626166066;G:1693802223;T:1820178560;N:616395,150,150,,,1879937256,1626166066,1693802223,1820178560,616395,ERX4769932,ERS5427208,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.92352,0.92388,0.04778,0.04768,0.6924,0.69205,0.45557,0.45865,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9963,ERR4902959,ERX4769931,ERS5427206,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae uninjected.,CRISPR RNAseq,SAMEA7670214,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670214|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq7|common name:zebrafish|sample name:CRISPR RNAseq7,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,WT1_R1_001.fastq.gz WT1_R2_001.fastq.gz,fastq fastq,5664550800.0,18881836.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 7,0:150 1:150,A:1493322675;C:1337347146;G:1388414458;T:1444981758;N:484763,150,150,,,1493322675,1337347146,1388414458,1444981758,484763,ERX4769931,ERS5427206,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95767,0.95821,0.04411,0.04384,0.69944,0.69944,0.44168,0.45263,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9964,ERR4902958,ERX4769930,ERS5427204,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670212,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670212|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq6|common name:zebrafish|sample name:CRISPR RNAseq6,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA3_R1_001.fastq.gz RNA3_R2_001.fastq.gz,fastq fastq,5814764400.0,19382548.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 6,0:150 1:150,A:1550014255;C:1359566801;G:1419514658;T:1485169819;N:498867,150,150,,,1550014255,1359566801,1419514658,1485169819,498867,ERX4769930,ERS5427204,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96165,0.96177,0.04961,0.04952,0.68183,0.68142,0.45636,0.46565,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9965,ERR4902957,ERX4769929,ERS5427203,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670211,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670211|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq5|common name:zebrafish|sample name:CRISPR RNAseq5,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA2_R1_001.fastq.gz RNA2_R2_001.fastq.gz,fastq fastq,5927606100.0,19758687.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 5,0:150 1:150,A:1579767222;C:1387675810;G:1439122138;T:1520529396;N:511534,150,150,,,1579767222,1387675810,1439122138,1520529396,511534,ERX4769929,ERS5427203,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.96212,0.96213,0.0519,0.05167,0.67099,0.6715,0.46875,0.47089,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9966,ERR4902956,ERX4769928,ERS5427201,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 mRNA.,CRISPR RNAseq,SAMEA7670209,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670209|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq4|common name:zebrafish|sample name:CRISPR RNAseq4,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,RNA1_R1_001.fastq.gz RNA1_R2_001.fastq.gz,fastq fastq,5738133000.0,19127110.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 4,0:150 1:150,A:1530616107;C:1342298453;G:1401357126;T:1463360623;N:500691,150,150,,,1530616107,1342298453,1401357126,1463360623,500691,ERX4769928,ERS5427201,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95706,0.9569,0.05122,0.05151,0.68757,0.68822,0.46039,0.4732,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9967,ERR4902955,ERX4769927,ERS5427199,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670207,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670207|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq3|common name:zebrafish|sample name:CRISPR RNAseq3,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO3_R1_001.fastq.gz PRO3_R2_001.fastq.gz,fastq fastq,9635841900.0,32119473.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:139 3,0:150 1:150,A:2562857735;C:2253487693;G:2325345541;T:2493627020;N:523911,150,150,,,2562857735,2253487693,2325345541,2493627020,523911,ERX4769927,ERS5427199,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95766,0.95695,0.05445,0.05404,0.67432,0.67403,0.46385,0.46442,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9968,ERR4902954,ERX4769926,ERS5427197,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670205,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670205|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq2|common name:zebrafish|sample name:CRISPR RNAseq2,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO2_R1_001.fastq.gz PRO2_R2_001.fastq.gz,fastq fastq,8990649900.0,29968833.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 2,0:150 1:150,A:2370044440;C:2140400380;G:2185347925;T:2294361536;N:495619,150,150,,,2370044440,2140400380,2185347925,2294361536,495619,ERX4769926,ERS5427197,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95444,0.95393,0.05848,0.05894,0.67438,0.67255,0.4825,0.48028,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
9969,ERR4902953,ERX4769925,ERS5427195,ERP123184,PRJEB39643,CRISPR tools for zebrafish,ena-STUDY-UNIVERSITY OF CALIFORNIA - DAVIS-29-07-2020-18:23:16:380-2095,Other,Zebrafish have practical features that make them a useful model for higher throughput tests of gene function using CRISPR/Cas9 editing to create 'knockout' models. A large number of computational and empirical tools exist to design CRISPR assays but often produce varied predictions across methods. To systematically assess accuracy of tool predictions of on  and off target gene editing  we subjected zebrafish embryos to CRISPR/Cas9 with 50 different guide RNAs gRNAs targeting 14 genes. We compared our experimental in vivo editing efficiencies in mosaic G0 embryos with those predicted by seven commonly used gRNA design tools and found large discrepancies between methods. Assessing off target mutations predicted in silico and in vitro found that the majority of tested loci had low in vivo frequencies <1%. To characterize if commonly used 'mock' CRISPR controls larvae injected with Cas9 enzyme or mRNA with no gRNA exhibited spurious molecular features that might exacerbate studies of G0 mosaic CRISPR knockout fish  we generated an RNA seq dataset of various control larvae at 5 dpf From this  while we found no evidence of spontaneous somatic mutations of injected larvae  we did identify several hundreds of differentially expressed genes with high variability between injection types. Network analyses of shared differentially expressed genes in the 'mock' injected larvae implicated a number of key regulators of common metabolic pathways  and gene ontology analysis revealed connections with response to wounding and cytoskeleton organization  highlighting a potential lasting effect from the microinjection process that requires further investigation. Overall  our results provide a valuable resource for the zebrafish community for the design and execution of CRISPR/Cas9 experiments.,ENA FIRST PUBLIC:2020 10 31|ENA LAST UPDATE:2021 05 25,,RNAseq data from 5dpf NHGRI 1 zebrafish larvae injected with Cas9 enzyme.,CRISPR RNAseq,SAMEA7670203,UNIVERSITY OF CALIFORNIA - DAVIS,ENA first public:2020 12 02|ENA last update:2020 12 02|External Id:SAMEA7670203|INSDC center alias:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC center name:UNIVERSITY OF CALIFORNIA   DAVIS|INSDC first public:2020 12 02T08:08:09Z|INSDC last update:2020 12 02T07:46:11Z|INSDC status:public|Submitter Id:CRISPR RNAseq1|common name:zebrafish|sample name:CRISPR RNAseq1,,,,,,,,,Illumina MiSeq paired end sequencing,ena EXPERIMENT UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1,unspecified,1,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina MiSeq,,ERP123184,Illumina MiSeq paired end sequencing,ENA FIRST PUBLIC:2020 12 02|ENA LAST UPDATE:2020 12 09,PRO1_R1_001.fastq.gz PRO1_R2_001.fastq.gz,fastq fastq,8803789500.0,29345965.0,ena RUN UNIVERSITY OF CALIFORNIA   DAVIS 02 12 2020 07:26:18:138 1,0:150 1:150,A:2318913314;C:2090675347;G:2149054140;T:2244296747;N:849952,150,150,,,2318913314,2090675347,2149054140,2244296747,849952,ERX4769925,ERS5427195,ERA3183786,UNIVERSITY OF CALIFORNIA - DAVIS|European Nucleotide Archive,UNIVERSITY OF CALIFORNIA - DAVIS,2,0.95403,0.95489,0.04655,0.0464,0.70816,0.71403,0.45357,0.44874,150,150,B,B,biological fallback assumption,illumina,miseq,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2020-10-31,Larval,Larval,Undetermined,Undetermined
25162,SRR25655085,SRX21381122,SRS18622091,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 8 AU1038 STRSS4,GSM7712891,,source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing,Sample 8 AU1038 STRSS4,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:From parent chronically stressed,GSM7712891,GSM7712891: Sample 8 AU1038 STRSS4; Danio rerio; ncRNA Seq,GSM7712891 r1,GSM7712891,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,STRS04_10932AAD_TGTCCTAC-ACATGAGT_R1_001.fastq.gz,fastq,641236400.0,12824728.0,GSM7712891 r1,0:50,A:183546979;C:159774155;G:156033079;T:141881902;N:285,50,,,,183546979,159774155,156033079,141881902,285,SRX21381122,SRS18622091,SRA1693666,CNAG,CNAG,1,0.4736,,0.03992,,0.96788,,0.87662,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25163,SRR25655086,SRX21381121,SRS18622090,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 7 AU1037 STRSS3,GSM7712890,,source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing,Sample 7 AU1037 STRSS3,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:From parent chronically stressed,GSM7712890,GSM7712890: Sample 7 AU1037 STRSS3; Danio rerio; ncRNA Seq,GSM7712890 r1,GSM7712890,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,STRS03_10931AAD_GCACGATT-CGTCTGCA_R1_001.fastq.gz,fastq,434646850.0,8692937.0,GSM7712890 r1,0:50,A:126760670;C:102577685;G:109591447;T:95716876;N:172,50,,,,126760670,102577685,109591447,95716876,172,SRX21381121,SRS18622090,SRA1693666,CNAG,CNAG,1,0.52132,,0.04615,,0.96477,,0.85481,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25164,SRR25655087,SRX21381120,SRS18622089,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 6 AU1036 STRSS2,GSM7712889,,source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing,Sample 6 AU1036 STRSS2,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:From parent chronically stressed,GSM7712889,GSM7712889: Sample 6 AU1036 STRSS2; Danio rerio; ncRNA Seq,GSM7712889 r1,GSM7712889,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,STRS02_10930AAD_ATGAAGCG-GCGGACAG_R1_001.fastq.gz,fastq,907610650.0,18152213.0,GSM7712889 r1,0:50,A:271494673;C:215304417;G:220608756;T:200202267;N:537,50,,,,271494673,215304417,220608756,200202267,537,SRX21381120,SRS18622089,SRA1693666,CNAG,CNAG,1,0.44189,,0.03477,,0.97335,,0.88092,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25165,SRR25655088,SRX21381119,SRS18622088,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 5 AU1035 STRSS1,GSM7712888,,source name:larvae|tissue:larvae|genotype:WT|treatment:From parent chronically stressed|geo loc name:missing|collection date:missing,Sample 5 AU1035 STRSS1,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:From parent chronically stressed,GSM7712888,GSM7712888: Sample 5 AU1035 STRSS1; Danio rerio; ncRNA Seq,GSM7712888 r1,GSM7712888,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,STRS01_10929AAD_CACTTCGA-TAGGCTTC_R1_001.fastq.gz,fastq,711276100.0,14225522.0,GSM7712888 r1,0:50,A:207284968;C:173540770;G:172961619;T:157488473;N:270,50,,,,207284968,173540770,172961619,157488473,270,SRX21381119,SRS18622088,SRA1693666,CNAG,CNAG,1,0.47865,,0.03881,,0.97001,,0.87616,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25166,SRR25655089,SRX21381118,SRS18622087,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 4 AU1028 CTRL4,GSM7712887,,source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Sample 4 AU1028 CTRL4,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:Control,GSM7712887,GSM7712887: Sample 4 AU1028 CTRL4; Danio rerio; ncRNA Seq,GSM7712887 r1,GSM7712887,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,CTRL04_10928AAD_GACTAGGC-GCCTCGAC_R1_001.fastq.gz,fastq,568037350.0,11360747.0,GSM7712887 r1,0:50,A:165826590;C:133109854;G:141956673;T:127143732;N:501,50,,,,165826590,133109854,141956673,127143732,501,SRX21381118,SRS18622087,SRA1693666,CNAG,CNAG,1,0.48051,,0.0347,,0.97268,,0.87465,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25167,SRR25655090,SRX21381117,SRS18622086,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 3 AU1027 CTRL3,GSM7712886,,source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Sample 3 AU1027 CTRL3,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:Control,GSM7712886,GSM7712886: Sample 3 AU1027 CTRL3; Danio rerio; ncRNA Seq,GSM7712886 r1,GSM7712886,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,CTRL03_10927AAD_AGTATACT-CGAATCGG_R1_001.fastq.gz,fastq,651469300.0,13029386.0,GSM7712886 r1,0:50,A:191788726;C:154951271;G:161329211;T:143399936;N:156,50,,,,191788726,154951271,161329211,143399936,156,SRX21381117,SRS18622086,SRA1693666,CNAG,CNAG,1,0.45412,,0.04073,,0.96934,,0.88507,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25168,SRR25655091,SRX21381116,SRS18622085,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 2 AU1026 CTRL2,GSM7712885,,source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Sample 2 AU1026 CTRL2,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:Control,GSM7712885,GSM7712885: Sample 2 AU1026 CTRL2; Danio rerio; ncRNA Seq,GSM7712885 r1,GSM7712885,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,CTRL02_10926AAD_CCGCGTAG-TTCTGATT_R1_001.fastq.gz,fastq,754615100.0,15092302.0,GSM7712885 r1,0:50,A:217013981;C:184328493;G:188964773;T:164307508;N:345,50,,,,217013981,184328493,188964773,164307508,345,SRX21381116,SRS18622085,SRA1693666,CNAG,CNAG,1,0.48926,,0.04654,,0.96418,,0.8889,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
25169,SRR25655092,SRX21381115,SRS18622084,SRP455342,PRJNA1005926,miR 29a is downregulated in progenies derived from chronically stressed males,GSE240954,Transcriptome Analysis,To investigate the potential vertical transmission of chronic stress to the unexposed larvae  to report novel consequences of paternally inherited chronic stress at molecular level Overall design: We then performed small RNA seq profiling in the stress derived group and the control one.,,pubmed:37762407,,Sample 1 AU1024 CTRL1,GSM7712884,,source name:larvae|tissue:larvae|genotype:WT|treatment:Control|geo loc name:missing|collection date:missing,Sample 1 AU1024 CTRL1,Trimming with trim galore v0.6.6   length 16   stringency 10 Mapping with STAR v2.7.8a against GRCz11 Quantification with RSEM v1.3.0 using ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV raw counts,larvae,,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,tissue:larvae|genotype:WT|treatment:Control,GSM7712884,GSM7712884: Sample 1 AU1024 CTRL1; Danio rerio; ncRNA Seq,GSM7712884 r1,GSM7712884,1,RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis.,,ncRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP455342,,loader:fastq load.py,CTRL01_10925AAD_TTAGCCTA-AATCATCA_R1_001.fastq.gz,fastq,670580700.0,13411614.0,GSM7712884 r1,0:50,A:194653643;C:158916446;G:165941477;T:151068917;N:217,50,,,,194653643,158916446,165941477,151068917,217,SRX21381115,SRS18622084,SRA1693666,CNAG,CNAG,1,0.47093,,0.03457,,0.97187,,0.8867,,50,,B,,usable mapping rate,illumina,novaseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Spain,2023-08-16,Larval,Larval,Undetermined,Undetermined
30665,SRR28146891,SRX23777735,SRS20602700,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae svcv3,GSM8117450,,source name:larvae|tissue:larvae|genotype:WT|treatment:svcv infection|geo loc name:missing|collection date:missing,zebrafish larvae svcv3,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:svcv infection,GSM8117450,GSM8117450: zebrafish larvae svcv3; Danio rerio; RNA Seq,GSM8117450 r1,GSM8117450,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,svcv-3_2.fq.gz svcv-3_1.fq.gz,fastq fastq,7824213900.0,26080713.0,GSM8117450 r1,0:150 1:150,A:2100807223;C:1802289231;G:1810811829;T:2108526136;N:1779481,150,150,,,2100807223,1802289231,1810811829,2108526136,1779481,SRX23777735,SRS20602700,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94199,0.93838,0.11761,0.11642,0.65583,0.65871,0.48366,0.47547,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
30666,SRR28146892,SRX23777734,SRS20602699,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae svcv2,GSM8117449,,source name:larvae|tissue:larvae|genotype:WT|treatment:svcv infection|geo loc name:missing|collection date:missing,zebrafish larvae svcv2,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:svcv infection,GSM8117449,GSM8117449: zebrafish larvae svcv2; Danio rerio; RNA Seq,GSM8117449 r1,GSM8117449,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,svcv-2_2.fq.gz svcv-2_1.fq.gz,fastq fastq,7890114900.0,26300383.0,GSM8117449 r1,0:150 1:150,A:2100297658;C:1835529449;G:1843517846;T:2109043200;N:1726747,150,150,,,2100297658,1835529449,1843517846,2109043200,1726747,SRX23777734,SRS20602699,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94591,0.94384,0.11233,0.11235,0.65683,0.65934,0.477,0.47924,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
30667,SRR28146893,SRX23777733,SRS20602698,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae svcv1,GSM8117448,,source name:larvae|tissue:larvae|genotype:WT|treatment:svcv infection|geo loc name:missing|collection date:missing,zebrafish larvae svcv1,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:svcv infection,GSM8117448,GSM8117448: zebrafish larvae svcv1; Danio rerio; RNA Seq,GSM8117448 r1,GSM8117448,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,svcv-1_1.fq.gz svcv-1_2.fq.gz,fastq fastq,10699844400.0,35666148.0,GSM8117448 r1,0:150 1:150,A:2874259238;C:2464699540;G:2474659412;T:2883944709;N:2281501,150,150,,,2874259238,2464699540,2474659412,2883944709,2281501,SRX23777733,SRS20602698,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94238,0.941,0.11297,0.11345,0.65218,0.65518,0.47212,0.47861,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
30668,SRR28146894,SRX23777732,SRS20602697,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae con3,GSM8117447,,source name:larvae|tissue:larvae|genotype:WT|treatment:control|geo loc name:missing|collection date:missing,zebrafish larvae con3,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:control,GSM8117447,GSM8117447: zebrafish larvae con3; Danio rerio; RNA Seq,GSM8117447 r1,GSM8117447,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,con-3_1.fq.gz con-3_2.fq.gz,fastq fastq,8616379800.0,28721266.0,GSM8117447 r1,0:150 1:150,A:2293550185;C:2006833599;G:2013673644;T:2300275613;N:2046759,150,150,,,2293550185,2006833599,2013673644,2300275613,2046759,SRX23777732,SRS20602697,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94877,0.94658,0.1015,0.10113,0.65048,0.65121,0.47054,0.47086,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
30669,SRR28146895,SRX23777731,SRS20602696,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae con2,GSM8117446,,source name:larvae|tissue:larvae|genotype:WT|treatment:control|geo loc name:missing|collection date:missing,zebrafish larvae con2,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:control,GSM8117446,GSM8117446: zebrafish larvae con2; Danio rerio; RNA Seq,GSM8117446 r1,GSM8117446,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,con-2_2.fq.gz con-2_1.fq.gz,fastq fastq,10567761000.0,35225870.0,GSM8117446 r1,0:150 1:150,A:2819524224;C:2448903032;G:2461825171;T:2835088526;N:2420047,150,150,,,2819524224,2448903032,2461825171,2835088526,2420047,SRX23777731,SRS20602696,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94701,0.94516,0.11656,0.11665,0.65036,0.65289,0.46853,0.47084,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
30670,SRR28146896,SRX23777730,SRS20602695,SRP492278,PRJNA1081795,Spring viraemia of carp virus infection induces hypoxia response in zebrafish by stabilizing hif1a,GSE260453,Transcriptome Analysis,The hypoxia signaling pathway controls hypoxia adaptation and tolerance of organisms  which is regulated by multiple mechanisms. Viral infection elicits various pathophysiological responses in the host. However  whether viral infection can affect the hypoxia response is still largely unknown. In this study  we found that Spring viraemia of carp virus SVCV infection in zebrafish caused symptoms similar to those in zebrafish under hypoxic conditions. Further assays indicated that SVCV infection activated the hypoxia signaling pathway in zebrafish. In addition  SVCV infection caused increased glycolysis and ROS levels in cells. Mechanistically  SVCV G protein interacted with hif1a a/b and attenuated their K48 linked polyubiquitination  leading to their stabilization and subsequent enhancement of target gene expression. Moreover  treatment with the HIF1a specific inhibitor PX478 enhanced the antiviral ability against SVCV infection in zebrafish and zebrafish cells. This study reveals a relationship between SVCV infection and the hypoxia signaling pathway in fish  and provides a strategy for reducing the damage of viral disease in the aquaculture industry. Overall design: Zebrafish larvae were placed in disposable cell culture dishes 60 mm in diameter containing 4 mL of egg water  and 2 mL of SVCV 5.0×107 TCID50/mL was added into each dish. Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Three biological replicates were used for each sample. The transcriptome library for sequencing was generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L following manufacturer's protocol In order to ensure the quality of information analysis  the software fastp was used to remove the splice sequences  filter the low quality  N bases indicating that the base information could not be determined  and obtain high quality clean data. clean data  and the number of bases and sequences of the clean data were counted. At the same time  GC  Q20  Q30 content of the clean data were calculated GenePlus  Beijing  China. Heatmaps were generated using Multi Experiment Viewer MeV software. Gene Ontology GO enrichment analyses for the differentially expressed genes DEGs were performed using the cluster Profiler version 3.8.,,pubmed:39601573,,zebrafish larvae con1,GSM8117445,,source name:larvae|tissue:larvae|genotype:WT|treatment:control|geo loc name:missing|collection date:missing,zebrafish larvae con1,Briefly  mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fastp version 0.19.7 was used to perform basic statistics on the quality of the raw reads. The clean reads were then mapped to the mouse genome using HISAT. Assembly: GRCz11 Supplementary files format and content: FPKM values for each Sample,larvae,,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer’s protocol  and index codes were added to assign sequences to each sample.,,tissue:larvae|genotype:WT|treatment:control,GSM8117445,GSM8117445: zebrafish larvae con1; Danio rerio; RNA Seq,GSM8117445 r1,GSM8117445,1,Whole RNA of zebrafish larvae 3 dpf infected with or without xxx were purified using RNeasy Mini Kit QIAGEN NO. 74104. Sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina NEB  USA  #E7530L accordingly to the manufacturer's protocol  and index codes were added to assign sequences to each sample.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP492278,,,con-1_1.fq.gz con-1_2.fq.gz,fastq fastq,7591748100.0,25305827.0,GSM8117445 r1,0:150 1:150,A:2040549045;C:1746495015;G:1755221657;T:2047720760;N:1761623,150,150,,,2040549045,1746495015,1755221657,2047720760,1761623,SRX23777730,SRS20602695,SRA1812384,????????????,中国科学院水生生物研究所,2,0.94625,0.9439,0.11156,0.11148,0.64482,0.64739,0.46845,0.46678,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,nebnext,bulk,unknown,unknown,,China,2024-02-28,Larval,Larval,Undetermined,Undetermined
31514,SRR28435337,SRX24039257,SRS20832031,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,cry dash /  group 2 at CT 16,Cryd CT16G2,Unknown BA023 04T0008.fq.gz,,isolate:The second group of cry dash /  fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0008.fq.gz,Unknown BA023 04T0008.fq.gz,CT16 cry dash group2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0008_good_2.fq.gz Unknown_BA023-04T0008_good_1.fq.gz,fastq fastq,6928082472.0,23162452.0,Unknown BA023 04T0008 good 1.fq.gz,0:149.55 1:149.55,A:1783381005;C:1671764458;G:1686432861;T:1786331460;N:172688,149,149,,,1783381005,1671764458,1686432861,1786331460,172688,SRX24039257,SRS20832031,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.96107,0.96048,0.06638,0.06578,0.68546,0.68582,0.46626,0.45803,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31515,SRR28435338,SRX24039256,SRS20832030,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,cry dash /  group 1 at CT 16,Cryd CT16G1,Unknown BA023 04T0007.fq.gz,,isolate:The first group of cry dash /  fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0007.fq.gz,Unknown BA023 04T0007.fq.gz,CT16 cry dash group1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0007_good_2.fq.gz Unknown_BA023-04T0007_good_1.fq.gz,fastq fastq,7247045982.0,24239568.0,Unknown BA023 04T0007 good 1.fq.gz,0:149.49 1:149.49,A:1868252704;C:1747715656;G:1761213537;T:1869681292;N:182793,149,149,,,1868252704,1747715656,1761213537,1869681292,182793,SRX24039256,SRS20832030,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.95954,0.95937,0.0624,0.06218,0.68809,0.68765,0.47347,0.47429,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31516,SRR28435339,SRX24039255,SRS20832029,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,cry dash /  group 2 at CT 4,Cryd CT4G2,Unknown BA023 04T0006.fq.gz,,isolate:The second group of cry dash /  fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0006.fq.gz,Unknown BA023 04T0006.fq.gz,CT4 cry dash group2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0006_good_1.fq.gz Unknown_BA023-04T0006_good_2.fq.gz,fastq fastq,7467294282.0,24985127.0,Unknown BA023 04T0006 good 1.fq.gz,0:149.43 1:149.43,A:1940430660;C:1790773066;G:1798765445;T:1937139187;N:185924,149,149,,,1940430660,1790773066,1798765445,1937139187,185924,SRX24039255,SRS20832029,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.95702,0.95753,0.08848,0.08877,0.6829,0.68199,0.49417,0.49443,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31517,SRR28435340,SRX24039254,SRS20832028,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,cry dash /  group 1 at CT 4,Cryd CT4G1,Unknown BA023 04T0005.fq.gz,,isolate:The first group of cry dash /  fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:cry dash / |health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0005.fq.gz,Unknown BA023 04T0005.fq.gz,CT4 cry dash group1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0005_good_1.fq.gz Unknown_BA023-04T0005_good_2.fq.gz,fastq fastq,6766310740.0,22646274.0,Unknown BA023 04T0005 good 1.fq.gz,0:149.39 1:149.39,A:1762324132;C:1615995203;G:1625767974;T:1762055354;N:168077,149,149,,,1762324132,1615995203,1625767974,1762055354,168077,SRX24039254,SRS20832028,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.95588,0.95587,0.06663,0.06633,0.67911,0.67888,0.46701,0.47626,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31518,SRR28435341,SRX24039253,SRS20832027,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,WT group 2 at CT 16,WT CT16G2,Unknown BA023 04T0004.fq.gz,,isolate:The second group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0004.fq.gz,Unknown BA023 04T0004.fq.gz,CT6 WT group2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0004_good_2.fq.gz Unknown_BA023-04T0004_good_1.fq.gz,fastq fastq,6830283170.0,22847843.0,Unknown BA023 04T0004 good 1.fq.gz,0:149.47 1:149.47,A:1791839697;C:1618554485;G:1627518993;T:1792199298;N:170697,149,149,,,1791839697,1618554485,1627518993,1792199298,170697,SRX24039253,SRS20832027,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.9515,0.94997,0.08493,0.08422,0.67178,0.67316,0.47915,0.48187,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31519,SRR28435342,SRX24039252,SRS20832026,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,WT group 1 at CT 16,WT CT16G1,Unknown BA023 04T0003.fq.gz,,isolate:The first group of WT fish collected at CT 16.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0003.fq.gz,Unknown BA023 04T0003.fq.gz,CT6 WT group1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0003_good_1.fq.gz Unknown_BA023-04T0003_good_2.fq.gz,fastq fastq,6430546584.0,21512133.0,Unknown BA023 04T0003 good 1.fq.gz,0:149.46 1:149.46,A:1678015842;C:1530296350;G:1541505212;T:1680568743;N:160437,149,149,,,1678015842,1530296350,1541505212,1680568743,160437,SRX24039252,SRS20832026,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.94974,0.95051,0.08145,0.0819,0.6775,0.67848,0.47999,0.47986,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31520,SRR28435343,SRX24039251,SRS20832025,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,WT group 2 at CT 4,WT CT4G2,Unknown BA023 04T0002.fq.gz,,isolate:The second group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0002.fq.gz,Unknown BA023 04T0002.fq.gz,CT4 WT group2,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0002_good_1.fq.gz Unknown_BA023-04T0002_good_2.fq.gz,fastq fastq,7084078326.0,23701315.0,Unknown BA023 04T0002 good 1.fq.gz,0:149.44 1:149.44,A:1855453089;C:1679520129;G:1688607029;T:1860319577;N:178502,149,149,,,1855453089,1679520129,1688607029,1860319577,178502,SRX24039251,SRS20832025,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.95393,0.95431,0.07799,0.07802,0.66728,0.66835,0.46237,0.47322,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31521,SRR28435344,SRX24039250,SRS20832024,SRP497569,PRJNA1090643,Danio rerio Raw sequence reads,PRJNA1090643,Other,The transcriptome of WT and cry dash /  mutant are tested at CT 4 and CT 16.,,,WT group 1 at CT 4,WT CT4G1,Unknown BA023 04T0001.fq.gz,,isolate:The first group of WT fish collected at CT 4.|age:120 hpf|collection date:2023 06 10|geo loc name:China:Suzhou|sex:not determined|tissue:larvae|biomaterial provider:Han Wang|birth date:2023 06 05|genotype:wildtype|health state:Health|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: larvae,Unknown BA023 04T0001.fq.gz,Unknown BA023 04T0001.fq.gz,CT4 WT group1,,,RNA-Seq,TRANSCRIPTOMIC,size fractionation,PAIRED,ILLUMINA,HiSeq X Five,,SRP497569,,,Unknown_BA023-04T0001_good_2.fq.gz Unknown_BA023-04T0001_good_1.fq.gz,fastq fastq,7360015710.0,24625447.0,Unknown BA023 04T0001 good 1.fq.gz,0:149.44 1:149.44,A:1931324589;C:1743134275;G:1748699685;T:1936672740;N:184421,149,149,,,1931324589,1743134275,1748699685,1936672740,184421,SRX24039250,SRS20832024,SRA1832685,Soochow University|School of Biology &amp; Basic Medical Sciences,Soochow University,2,0.954,0.95301,0.08257,0.08182,0.66772,0.66906,0.47505,0.47577,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,size_fractionation,unknown,bulk,unknown,unknown,,Unknown,2024-03-25,Larval,Larval,Undetermined,Undetermined
31825,SRR28700412,SRX24268115,SRS21034395,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,PN 2,,isolate:PN2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,PN 2,PN 2,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,PN_2_1.fq.gz PN_2_2.fq.gz,fastq fastq,6385048200.0,21283494.0,PN 2 1.fq.gz,0:150 1:150,A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0,150,150,,,1722127999,1463645587,1483173818,1716100796,0,SRX24268115,SRS21034395,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31826,SRR28700413,SRX24268114,SRS21034397,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,PN 1,,isolate:PN1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,PN 1,PN 1,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,PN_1_1.fq.gz PN_1_2.fq.gz,fastq fastq,6692894100.0,22309647.0,PN 1 1.fq.gz,0:150 1:150,A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0,150,150,,,1827107021,1513034624,1533077624,1819674831,0,SRX24268114,SRS21034397,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31827,SRR28700414,SRX24268113,SRS21034396,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,EC 4,,isolate:EC4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,EC 4,EC 4,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,EC_4_1.fq.gz EC_4_2.fq.gz,fastq fastq,6688857000.0,22296190.0,EC 4 1.fq.gz,0:150 1:150,A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0,150,150,,,1820989545,1516814697,1537970654,1813082104,0,SRX24268113,SRS21034396,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31828,SRR28700415,SRX24268112,SRS21034392,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,EC 3,,isolate:EC3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,EC 3,EC 3,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,EC_3_1.fq.gz EC_3_2.fq.gz,fastq fastq,6696553800.0,22321846.0,EC 3 1.fq.gz,0:150 1:150,A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0,150,150,,,1821249100,1520587242,1541238550,1813478908,0,SRX24268112,SRS21034392,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31829,SRR28700416,SRX24268111,SRS21034391,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,EC 2,,isolate:EC2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,EC 2,EC 2,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,EC_2_1.fq.gz EC_2_2.fq.gz,fastq fastq,6702179400.0,22340598.0,EC 2 1.fq.gz,0:150 1:150,A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0,150,150,,,1816692261,1527379142,1547365810,1810742187,0,SRX24268111,SRS21034391,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31830,SRR28700417,SRX24268110,SRS21034390,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,EC 1,,isolate:EC1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,EC 1,EC 1,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,EC_1_1.fq.gz EC_1_2.fq.gz,fastq fastq,6686053500.0,22286845.0,EC 1 1.fq.gz,0:150 1:150,A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0,150,150,,,1812022780,1524359858,1544847441,1804823421,0,SRX24268110,SRS21034390,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31831,SRR28700418,SRX24268109,SRS21034388,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,Control 4,,isolate:con4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,Control 4,Control 4,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,Control_4_1.fq.gz Control_4_2.fq.gz,fastq fastq,6669700500.0,22232335.0,Control 4 1.fq.gz,0:150 1:150,A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0,150,150,,,1804178265,1523547469,1543839484,1798135282,0,SRX24268109,SRS21034388,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31832,SRR28700419,SRX24268108,SRS21034387,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,Control 3,,isolate:con3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,Control 3,Control 3,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,Control_3_1.fq.gz Control_3_2.fq.gz,fastq fastq,6683518800.0,22278396.0,Control 3 1.fq.gz,0:150 1:150,A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0,150,150,,,1808495506,1525725204,1545930043,1803368047,0,SRX24268108,SRS21034387,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31833,SRR28700420,SRX24268107,SRS21034386,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,PN 4,,isolate:PN4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,PN 4,PN 4,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,PN_4_1.fq.gz PN_4_2.fq.gz,fastq fastq,6649316100.0,22164387.0,PN 4 1.fq.gz,0:150 1:150,A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0,150,150,,,1809816121,1508072480,1528272654,1803154845,0,SRX24268107,SRS21034386,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31834,SRR28700421,SRX24268106,SRS21034389,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,PN 3,,isolate:PN3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,PN 3,PN 3,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,PN_3_1.fq.gz PN_3_2.fq.gz,fastq fastq,6616113900.0,22053713.0,PN 3 1.fq.gz,0:150 1:150,A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0,150,150,,,1802283686,1499008018,1519150002,1795672194,0,SRX24268106,SRS21034389,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31835,SRR28700422,SRX24268105,SRS21034385,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,Control 2,,isolate:con2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,Control 2,Control 2,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,Control_2_1.fq.gz Control_2_2.fq.gz,fastq fastq,6701719200.0,22339064.0,Control 2 1.fq.gz,0:150 1:150,A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0,150,150,,,1812352260,1531672703,1551377072,1806317165,0,SRX24268105,SRS21034385,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31836,SRR28700423,SRX24268104,SRS21034384,SRP501894,PRJNA1100624,Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis,PRJNA1100624,Other,Research indicates that Epimedin C EC  an active compound in Epimedium  offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization  increases bone mass  and improves bone density  thus mitigating bone tissue damage caused by prednisolone. Additionally  EC impacts key signaling pathways related to bone development  such as osteoclast differentiation  estrogen  MAPK  insulin resistance  PPAR  and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects  presenting it as a viable  cost effective treatment for GIOP.,,,,,Control 1,,isolate:con1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish,Control 1,Control 1,Total RNA undergoes mRNA enrichment  reverse transcription  adapter ligation  PCR amplification  and circularization into a single stranded DNA library.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,BGISEQ,BGISEQ-500,,SRP501894,,,Control_1_1.fq.gz Control_1_2.fq.gz,fastq fastq,6720214500.0,22400715.0,Control 1 1.fq.gz,0:150 1:150,A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0,150,150,,,1814883015,1537948710,1559376116,1808006659,0,SRX24268104,SRS21034384,,,"Xiangyang No.1 People's Hospital, Hubei University of Medicine",,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-04-15,Larval,Larval,Undetermined,Undetermined
31937,SRR28787280,SRX24351570,SRS21110452,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,p2ry11 mutant 3,GSM8225399,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf knockout|geo loc name:missing|collection date:missing,p2ry11 mutant 3,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf knockout,GSM8225399,GSM8225399: p2ry11 mutant 3; Danio rerio; RNA Seq,GSM8225399 r1,GSM8225399,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,P2RY11-3_R1.fastq.gz P2RY11-3_R2.fastq.gz,fastq fastq,7281756000.0,24272520.0,GSM8225399 r1,0:150 1:150,A:2000834135;C:1632282704;G:1700870245;T:1947708842;N:60074,150,150,,,2000834135,1632282704,1700870245,1947708842,60074,SRX24351570,SRS21110452,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
31938,SRR28787281,SRX24351569,SRS21110451,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,p2ry11 mutant 2,GSM8225398,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf knockout|geo loc name:missing|collection date:missing,p2ry11 mutant 2,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf knockout,GSM8225398,GSM8225398: p2ry11 mutant 2; Danio rerio; RNA Seq,GSM8225398 r1,GSM8225398,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,P2RY11-2_R1.fastq.gz P2RY11-2_R2.fastq.gz,fastq fastq,6847717800.0,22825726.0,GSM8225398 r1,0:150 1:150,A:1842749199;C:1569275764;G:1649037745;T:1786599153;N:55939,150,150,,,1842749199,1569275764,1649037745,1786599153,55939,SRX24351569,SRS21110451,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
31939,SRR28787282,SRX24351568,SRS21110450,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,p2ry11 mutant 1,GSM8225397,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf knockout|geo loc name:missing|collection date:missing,p2ry11 mutant 1,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf knockout,GSM8225397,GSM8225397: p2ry11 mutant 1; Danio rerio; RNA Seq,GSM8225397 r1,GSM8225397,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,P2RY11-1_R1.fastq.gz P2RY11-1_R2.fastq.gz,fastq fastq,5685382800.0,18951276.0,GSM8225397 r1,0:150 1:150,A:1533315499;C:1304492938;G:1330805028;T:1516720683;N:48652,150,150,,,1533315499,1304492938,1330805028,1516720683,48652,SRX24351568,SRS21110450,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
31940,SRR28787283,SRX24351567,SRS21110449,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,WT Sibling Control 3,GSM8225396,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf loc name:missing|collection date:missing,WT Sibling Control 3,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf,GSM8225396,GSM8225396: WT Sibling Control 3; Danio rerio; RNA Seq,GSM8225396 r1,GSM8225396,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,WT3_R1.fastq.gz WT3_R2.fastq.gz,fastq fastq,9096111900.0,30320373.0,GSM8225396 r1,0:150 1:150,A:2474201653;C:2071402500;G:2128229187;T:2422144410;N:134150,150,150,,,2474201653,2071402500,2128229187,2422144410,134150,SRX24351567,SRS21110449,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
31941,SRR28787284,SRX24351566,SRS21110448,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,WT Sibling Control 2,GSM8225395,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf loc name:missing|collection date:missing,WT Sibling Control 2,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf,GSM8225395,GSM8225395: WT Sibling Control 2; Danio rerio; RNA Seq,GSM8225395 r1,GSM8225395,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,WT2_R1.fastq.gz WT2_R2.fastq.gz,fastq fastq,9073457700.0,30244859.0,GSM8225395 r1,0:150 1:150,A:2377620319;C:2148477327;G:2213637714;T:2333593535;N:128805,150,150,,,2377620319,2148477327,2213637714,2333593535,128805,SRX24351566,SRS21110448,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
31942,SRR28787285,SRX24351565,SRS21110447,SRP503694,PRJNA1103784,Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish,GSE264674,Transcriptome Analysis,Purinergic receptor P2Y11  a G protein coupled receptor that is stimulated by the endogenous ATP  has been demonstrated to be related with the chemotaxis of granulocytes  apoptosis of neutrophils  and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However  little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study  we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function  we performed GO term analysis of the up regulated and down regulated DE genes of P2RY11 8bp versus their WT controls. The results showed that plasma membrane signaling receptor complex GO:0098802  calcium ion binding GO:0005509  and protein refolding GO:0042026 were most enriched terms in up regulated DE genes. While metabolic process GO:008152  location Go:0051179 and cellular process GO:009987 were most enriched terms in down regulated DE genes . In addition  immune system process GO:0002376 was also enriched in down regulated DE genes of P2RY11 8bp versus WT controls . Basic on the genes related with immune system process  we further performed GO term enrichment analysis and found that the defense response  leukocyte chemiotaxis  and inflammatory response were the main enriched terms. Overall design: The p2ry11 /  mutant and  wild type WT sibling were produced from p2ry11 heterozygous +/  intercross embryos. Subsequently  RNA was extracted from the p2ry11 /  mutant and the WT sibling embryos using TRIzol reagent.We then performed gene expression profiling analysis using data obtained from RNA seq of the mutant and WT siblings.,,pubmed:38771396,,WT Sibling Control 1,GSM8225394,,source name:zebrafish larvae|tissue:zebrafish larvae|time:3 dpf loc name:missing|collection date:missing,WT Sibling Control 1,Image analysis and base calling were performed using Solexa pipeline v1.8 Off Line Base Caller software  v1.8 Sequence quality was examined using the FastQC softwarev0.11.7 The trimmed reads trimmed 5’  3’ adaptor bases using cutadaptv1.17 were aligned to reference genomeGRCh37 using Hisat2 softwarev2.1.0 The transcript abundance for each sample was estimated with StringTiev1.3.3  and the FPKM value for gene and transcript level was calculated with R package Ballgownv2.10.0 Assembly: GRCh37 Supplementary files format and content: the FPKM value of detected mRNA for each sample,zebrafish larvae,,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,Larvae were kept in E3 medium with methylene blue at 28.5°C,tissue:zebrafish larvae|time:3 dpf,GSM8225394,GSM8225394: WT Sibling Control 1; Danio rerio; RNA Seq,GSM8225394 r1,GSM8225394,1,RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP503694,,loader:fastq load.py,WT1_R1.fastq.gz WT1_R2.fastq.gz,fastq fastq,8603955300.0,28679851.0,GSM8225394 r1,0:150 1:150,A:2240309294;C:2049376665;G:2129411026;T:2184731732;N:126583,150,150,,,2240309294,2049376665,2129411026,2184731732,126583,SRX24351565,SRS21110447,SRA1851694,???,医学院,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Unknown,2024-04-23,Larval,Larval,Undetermined,Undetermined
33350,SRR30136585,SRX25605812,SRS22254471,SRP524293,PRJNA1143173,Toxic mechanism of the novel pesticide pyrifluquinazon PFQ and its major metabolite in early life stage zebrafish,PRJNA1143173,Other,To investigate the mechanisms underlying the developmental toxicity of PFQ and dPFQ in zebrafish early life stage  RNA seq and transcriptomic analyses were conducted. For the solvent control  middle and high concentration groups of PFQ and dPFQ exposure  3 biological replicates were included  making 15 samples in total. The sequencing was performed by Novogene Co.  Ltd.  China.,,,14,,01H2,,strain:WILD|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:larvae|collection date:2022 11 20|geo loc name:China|sex:not determined|tissue:larvae|replicate:dPFQ H replicate biological 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of daniorerio,01H2,01H2,Illumina NovaSeq 6000,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP524293,,,01H2_1.fq.gz 01H2_2.fq.gz,fastq fastq,6313056900.0,21043523.0,01H2 1.fq.gz,0:150 1:150,A:1766006943;C:1407384164;G:1393123543;T:1746425506;N:116744,150,150,,,1766006943,1407384164,1393123543,1746425506,116744,SRX25605812,SRS22254471,SRA1939705,Research Center for Eco-Environmental Sciences|University of Chinese Academy of Sciences,Research Center for Eco-Environmental Sciences,2,0.85886,0.85703,0.20363,0.20144,0.74044,0.74249,0.55406,0.5549,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-08-05,Larval,Larval,Undetermined,Undetermined
33369,SRR30159204,SRX25626516,SRS22271512,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Mutant 2,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.8 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Mutant 2,Li lab 003 4,Li lab 003 4,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 6 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,7c166f592635e7a5f904d56dd661e1cc mut-2_1.fq.gz.gz 3adc1733ac4cb77beca49461cb17544b mut-2_2.fq.gz.gz,fastq fastq,5518961400.0,18396538.0,3adc1733ac4cb77beca49461cb17544b mut 2 2.fq.gz.gz,0:150 1:150,A:1469924277;C:1285547670;G:1307420673;T:1455990444;N:78336,150,150,,,1469924277,1285547670,1307420673,1455990444,78336,SRX25626516,SRS22271512,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96085,0.95919,0.05548,0.05519,0.7207,0.72178,0.47759,0.47549,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33370,SRR30159205,SRX25626515,SRS22271511,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Mutant 1,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.7 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Mutant 1,Li lab 003 3,Li lab 003 3,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 5 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,39cb7947119cec5afac3df66c0ae0048 mut-1_1.fq.gz.gz 1bfc59902758bb1cbf8eb4549d3375fd mut-1_2.fq.gz.gz,fastq fastq,5947120500.0,19823735.0,1bfc59902758bb1cbf8eb4549d3375fd mut 1 2.fq.gz.gz,0:150 1:150,A:1567673549;C:1401761128;G:1423907629;T:1553701047;N:77147,150,150,,,1567673549,1401761128,1423907629,1553701047,77147,SRX25626515,SRS22271511,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96303,0.96203,0.05003,0.04984,0.72271,0.72299,0.47608,0.47831,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33371,SRR30159206,SRX25626514,SRS22271510,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Wild type 2,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.6 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Wild type 2,Li lab 003 2,Li lab 003 2,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 4 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,4376e7007befe0cf23ffa7f9dd62512c sib-3_1.fq.gz.gz da4d46fd26ca22e90409489640659b1c sib-3_2.fq.gz.gz,fastq fastq,6113935200.0,20379784.0,4376e7007befe0cf23ffa7f9dd62512c sib 3 1.fq.gz.gz,0:150 1:150,A:1609711214;C:1443384557;G:1461871812;T:1598876167;N:91450,150,150,,,1609711214,1443384557,1461871812,1598876167,91450,SRX25626514,SRS22271510,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.95947,0.9591,0.04902,0.0492,0.71707,0.71796,0.46871,0.4604,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
33372,SRR30159207,SRX25626513,SRS22271509,SRP524652,PRJNA1145276,The RNA sequence analysis post lossing tango6,PRJNA1145276,Other,To detect RNA expression level difference post lost of TANGO6,,,,,Wild type 1,,strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.5 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal,,,,,,,,,Wild type 1,Li lab 003 1,Li lab 003 1,RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 3 g of total RNA was used for construction of sequencing libraries.,,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP524652,,,319b2e8b61305a8937eb903a7a20a2e7 sib-2_1.fq.gz.gz 4a84982431b5360126f279ceabf00548 sib-2_2.fq.gz.gz,fastq fastq,6351813000.0,21172710.0,319b2e8b61305a8937eb903a7a20a2e7 sib 2 1.fq.gz.gz,0:150 1:150,A:1674596701;C:1497102731;G:1525030471;T:1654985592;N:97505,150,150,,,1674596701,1497102731,1525030471,1654985592,97505,SRX25626513,SRS22271509,SRA1941919,"Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing","Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences",2,0.96469,0.96334,0.04679,0.04633,0.73119,0.73198,0.47359,0.47265,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,other,unknown,bulk,unknown,unknown,,China,2024-08-07,Larval,Larval,Undetermined,Undetermined
34224,SRR31604147,SRX26968916,SRS23437614,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,CV mCherry negative,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Conventionalized|Fluorescence:mCherry negative  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from CV larvae,7066 P3,7066 P3,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,CV_IEC_3_S3_L001_I1_001.fastq.gz CV_IEC_3_S3_L001_R1_001.fastq.gz CV_IEC_3_S3_L001_R2_001.fastq.gz CV_IEC_3_S3_L002_I1_001.fastq.gz CV_IEC_3_S3_L002_R1_001.fastq.gz CV_IEC_3_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,39983364288.0,317328288.0,CV IEC 3 S3 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:7989957184;C:6492876848;G:7106881008;T:6968481488;N:1349392,8,28,90,,7989957184,6492876848,7106881008,6968481488,1349392,SRX26968916,SRS23437614,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34225,SRR31604148,SRX26968915,SRS23437613,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,GF mCherry negative,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Germ free|Fluorescence:mCherry negative  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry negative  GFP positive sorted cells from GF larvae,7066 P1,7066 P1,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,GF_IEC_1_S1_L001_I1_001.fastq.gz GF_IEC_1_S1_L001_R1_001.fastq.gz GF_IEC_1_S1_L001_R2_001.fastq.gz GF_IEC_1_S1_L002_I1_001.fastq.gz GF_IEC_1_S1_L002_R1_001.fastq.gz GF_IEC_1_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,40178994030.0,318880905.0,GF IEC 1 S1 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:8197955224;C:6448684398;G:7158064923;T:6893218597;N:1358308,8,28,90,,8197955224,6448684398,7158064923,6893218597,1358308,SRX26968915,SRS23437613,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34226,SRR31604149,SRX26968914,SRS23437612,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,CV mCherry positive,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Conventionalized|Fluorescence:mCherry positive  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from CV larvae,7066 P4,7066 P4,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,CV_LRE_4_S4_L001_I1_001.fastq.gz CV_LRE_4_S4_L001_R1_001.fastq.gz CV_LRE_4_S4_L001_R2_001.fastq.gz CV_LRE_4_S4_L002_I1_001.fastq.gz CV_LRE_4_S4_L002_R1_001.fastq.gz CV_LRE_4_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,19934299602.0,158208727.0,CV LRE 4 S4 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:4398648037;C:3082182233;G:3214972719;T:3542307593;N:674848,8,28,90,,4398648037,3082182233,3214972719,3542307593,674848,SRX26968914,SRS23437612,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34227,SRR31604150,SRX26968913,SRS23437611,SRP549343,PRJNA1192682,Microbial regulation of gene expression patterns in lysosome rich enterocyte LRE and intestinal epithelial cells,PRJNA1192682,Other,The goal of this study was to characterize the effects of the microbiome on gene expression patterns in lysosome rich enterocytes LREs and other intestinal epithelial cells IECs. Using transgene assisted cell isolation and single cell RNA sequencing  we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria sensing and metabolic pathways in LREs  and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs.,,,,,GF mCherry positive,,strain:EK|age:6 dpf|collection date:2021|geo loc name:USA: Durham  NC|sex:not applicable|tissue:Sorted cells|Condition:Germ free|Fluorescence:mCherry positive  GFP positive|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of danio rerio: mCherry positive  GFP positive sorted cells from GF larvae,7066 P2,7066 P2,TgBACcldn15la GFPpd1034 larvae were raised in GF and CV conditions to 6 dpf. CV and GF  GFP positive larvae were gavaged with mCherry to mark LREs with mCherry in addition to GFP. Larvae were dissociated  and cell suspensions were sorted by FACS. Library preparation was completed with the Chromium Next GEM Single Cell 3 GEM  Library & Gel Bead Kit v3.1.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP549343,,,GF_LRE_2_S2_L001_I1_001.fastq.gz GF_LRE_2_S2_L001_R1_001.fastq.gz GF_LRE_2_S2_L001_R2_001.fastq.gz GF_LRE_2_S2_L002_I1_001.fastq.gz GF_LRE_2_S2_L002_R1_001.fastq.gz GF_LRE_2_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq fastq fastq,16477189470.0,130771345.0,GF LRE 2 S2 L001 I1 001.fastq.gz,0:8 1:28 2:90,A:3664699916;C:2552676887;G:2506770636;T:3044709641;N:563970,8,28,90,,3664699916,2552676887,2506770636,3044709641,563970,SRX26968913,SRS23437611,SRA2025080,Duke University|Cell Biology,Duke University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-04,Larval,Larval,Undetermined,Undetermined
34282,SRR31640757,SRX27004210,SRS23468967,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 1,BXP 1,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP_1.fq.gz,fastq,816499035.0,16009785.0,BXP 1.fq.gz,0:51,A:191280900;C:189440771;G:247005615;T:188686493;N:85256,51,,,,191280900,189440771,247005615,188686493,85256,SRX27004210,SRS23468967,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34283,SRR31640758,SRX27004209,SRS23468966,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 3,Control 3,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control_3.fq.gz,fastq,662560023.0,12991373.0,Control 3.fq.gz,0:51,A:151053320;C:152811933;G:203340354;T:155283230;N:71186,51,,,,151053320,152811933,203340354,155283230,71186,SRX27004209,SRS23468966,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34284,SRR31640759,SRX27004208,SRS23468963,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 2,Control 2,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control_2.fq.gz,fastq,648856119.0,12722669.0,Control 2.fq.gz,0:51,A:149869576;C:151844056;G:195830503;T:151241215;N:70769,51,,,,149869576,151844056,195830503,151241215,70769,SRX27004208,SRS23468963,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34285,SRR31640760,SRX27004207,SRS23468962,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Control group,Control 1,Control 1,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control_1.fq.gz,fastq,835887501.0,16389951.0,Control 1.fq.gz,0:51,A:193253330;C:196900031;G:252690178;T:192797500;N:246462,51,,,,193253330,196900031,252690178,192797500,246462,SRX27004207,SRS23468962,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34286,SRR31640761,SRX27004206,SRS23468965,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 3,BXP 3,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-3_1.fq.gz BXP-3_2.fq.gz,fastq fastq,6830689200.0,22768964.0,BXP 3 1.fq.gz,0:150 1:150,A:1937590708;C:1484093984;G:1501320204;T:1907663118;N:21186,150,150,,,1937590708,1484093984,1501320204,1907663118,21186,SRX27004206,SRS23468965,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34287,SRR31640762,SRX27004205,SRS23468964,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 2,BXP 2,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-2_1.fq.gz BXP-2_2.fq.gz,fastq fastq,6779695800.0,22598986.0,BXP 2 1.fq.gz,0:150 1:150,A:1940362424;C:1457342925;G:1474251255;T:1907718219;N:20977,150,150,,,1940362424,1457342925,1474251255,1907718219,20977,SRX27004205,SRS23468964,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34288,SRR31640763,SRX27004204,SRS23468967,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Experiment group,BXP 1,BXP 1,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP-1_1.fq.gz BXP-1_2.fq.gz,fastq fastq,6565466100.0,21884887.0,BXP 1 1.fq.gz,0:150 1:150,A:1875205670;C:1413467668;G:1430939925;T:1845830468;N:22369,150,150,,,1875205670,1413467668,1430939925,1845830468,22369,SRX27004204,SRS23468967,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34289,SRR31640764,SRX27004203,SRS23468966,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 3,Control 3,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-3_1.fq.gz Control-3_2.fq.gz,fastq fastq,6430890900.0,21436303.0,Control 3 1.fq.gz,0:150 1:150,A:1836469770;C:1387135442;G:1409220900;T:1798042594;N:22194,150,150,,,1836469770,1387135442,1409220900,1798042594,22194,SRX27004203,SRS23468966,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34290,SRR31640765,SRX27004202,SRS23468965,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD3,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate3|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 3,BXP 3,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP_3.fq.gz,fastq,656139327.0,12865477.0,BXP 3.fq.gz,0:51,A:152349522;C:156353407;G:196379918;T:150985088;N:71392,51,,,,152349522,156353407,196379918,150985088,71392,SRX27004202,SRS23468965,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34291,SRR31640766,SRX27004201,SRS23468964,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,CD2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Experiment group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,microRNA seq of Danio rerio: Experiment group,BXP 2,BXP 2,,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,BXP_2.fq.gz,fastq,644434827.0,12635977.0,BXP 2.fq.gz,0:51,A:151820167;C:153674905;G:190467723;T:148402934;N:69098,51,,,,151820167,153674905,190467723,148402934,69098,SRX27004201,SRS23468964,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34292,SRR31640767,SRX27004200,SRS23468963,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control2,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 2,Control 2,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-2_1.fq.gz Control-2_2.fq.gz,fastq fastq,6980411100.0,23268037.0,Control 2 1.fq.gz,0:150 1:150,A:1967066686;C:1535551736;G:1553468906;T:1924299656;N:24116,150,150,,,1967066686,1535551736,1553468906,1924299656,24116,SRX27004200,SRS23468963,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-07,Undetermined,Larval,Undetermined,Undetermined
34293,SRR31640768,SRX27004199,SRS23468962,SRP550004,PRJNA1195374,Cortex Dictamni induces retinitis pigmentosa in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2,PRJNA1195374,Other,Ethnopharmacological relevance: Cortex Dictamni CD is the dried root skin of Dictamnus dasycarpus Turcz  widely used in the field of traditional Chinese medicine. mainly for the treatment of skin diseases. Recent adverse reactions to CD limited the clinical application in combination with other traditional Chinese medicines.Aim of the study: To investigate the retinitis pigmentosa RP effects of CD using the zebrafish model and elucidate the underlying molecular mechanism of CD induced RP in zebrafish.Materials and methods: The 3 dpf zebrafish larvae were divided into control and CD group. RNA sequencing followed  with qRT PCR validating miRNAs and mRNAs. Dual luciferase reporter assay confirmed mmu mir 6240 p3 2's interaction with pde6a. HT22 cells were transfected  treated with CD  and evaluated for migration  invasion  malondialdehyde level  superoxide dismutase and acetylcholine activities.Results: The results showed 6228 differentially expressed genes and 66 miRNAs differentially expressed in zebrafish exposed to CD. The personal correlation coefficient results showed that mmu mir 6240 p3 2 had the highest correlation coefficient with pde6a and had a negative regulatory relationship. The results of dual luciferase reporter gene further showed that pde6a gene was the direct target of mmu mir 6240 p3 2. Cell experiment results showed that inhibiting mir 6240 p3 2 can upregulate pde6a expression  alleviate HT22 cell injury  and reverse the inhibition of cell migration and invasion induced by CD.Conclusions: CD induces RP in zebrafish by inhibiting pde6a post transcriptional activity via mmu mir 6240 p3 2. These findings have important implications for understanding the potential side effects of CD and for developing safer therapeutic strategies involving traditional Chinese medicines.,,,,,Control1,,strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|collection date:not applicable|geo loc name:not applicable|sex:not applicable|tissue:not applicable|treatment:Control group replicate1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: Control group,Control 1,Control 1,,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP550004,,,Control-1_1.fq.gz Control-1_2.fq.gz,fastq fastq,6893069100.0,22976897.0,Control 1 1.fq.gz,0:150 1:150,A:1990628725;C:1465163855;G:1482329167;T:1954923719;N:23634,150,150,,,1990628725,1465163855,1482329167,1954923719,23634,SRX27004199,SRS23468962,SRA2029520,Heilongjiang University of Chinese Medicine|College of Traditional Chinese Medicine,Heilongjiang University of Chinese Medicine,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-12-09,Undetermined,Larval,Undetermined,Undetermined
34487,SRR31790708,SRX27151927,SRS23606412,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 2,GSM8695646,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695646,GSM8695646: RNA zebrafish larvae treated PM2.5 rep 2; Danio rerio; RNA Seq,GSM8695646 r1,GSM8695646,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_2_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_2_R2.fq.gz,fastq fastq,6499686900.0,21665623.0,GSM8695646 r1,0:150 1:150,A:1738791948;C:1515807515;G:1516684626;T:1724651740;N:3751071,150,150,,,1738791948,1515807515,1516684626,1724651740,3751071,SRX27151927,SRS23606412,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34488,SRR31790709,SRX27151926,SRS23606411,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae treated PM2.5 rep 1,GSM8695645,,source name:larvea|tissue:larvea|treatment:treatment with PM2.5|geo loc name:missing|collection date:missing,RNA zebrafish larvae treated PM2.5 rep 1,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:treatment with PM2.5,GSM8695645,GSM8695645: RNA zebrafish larvae treated PM2.5 rep 1; Danio rerio; RNA Seq,GSM8695645 r1,GSM8695645,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_treated_PM2.5_rep_1_R1.fq.gz RNA_zebrafish_larvae_treated_PM2.5_rep_1_R2.fq.gz,fastq fastq,10116536700.0,33721789.0,GSM8695645 r1,0:150 1:150,A:2712593040;C:2357036246;G:2349793342;T:2687696916;N:9417156,150,150,,,2712593040,2357036246,2349793342,2687696916,9417156,SRX27151926,SRS23606411,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34489,SRR31790710,SRX27151925,SRS23606410,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae control rep 2,GSM8695644,,source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing,RNA zebrafish larvae control rep 2,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:control,GSM8695644,GSM8695644: RNA zebrafish larvae control rep 2; Danio rerio; RNA Seq,GSM8695644 r1,GSM8695644,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_control_rep_2_R1.fq.gz RNA_zebrafish_larvae_control_rep_2_R2.fq.gz,fastq fastq,6347285700.0,21157619.0,GSM8695644 r1,0:150 1:150,A:1687168204;C:1494146408;G:1490096893;T:1672074832;N:3799363,150,150,,,1687168204,1494146408,1490096893,1672074832,3799363,SRX27151925,SRS23606410,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34490,SRR31790711,SRX27151924,SRS23606409,SRP552945,PRJNA1201093,Fine particulate matter PM2.5 induces microRNA 192–5p causing glomerular damage,GSE285038,Transcriptome Analysis,To unravel changes in gene expression due to exposure to PM2.5  we performed bulk RNA seq analyses of zebrafish larvae exposed to PM2.5 and controls. Among others  PM2.5 increased oxoglutarate alpha ketoglutarate receptor 1a  nitric oxide synthase  arachidonate 5 lipoxygenase b  immunity related GTPase family e1  sulfotransferase family 5A  and macrophage expressed 1. NADPH oxidase organizer 1a and NADPH oxidase 1 were upregulated due to PM2.5 exposure. Furthermore  protein tyrosine/serine/threonine phosphatase activity was decreased post exposure to PM2.5. GESA analysis showed that genes involved in proteasome complex formation  inflammatory and immune response  leucocyte mediated cytotoxicity  peptidase activator activity protein folding  and apoptotic signaling were upregulated post exposure to PM2.5. These results indicate that PM2.5 exposure caused the activation of immune inflammatory and oxidative stress pathways and lipid and metabolic dysregulation. Overall design: Zebrafish were mated at 28.5°C  and larvae grew in standard E3 solution. Zebrafish larvae were exposed to 1.2 × 10^7 smog particles from 72 hpf till 120 hpf. Untreated zebrafish larvae served as controls. RNA was isolated from 5 7 zebrafish larvae in each group. RNA from whole zebrafish was isolated using the ReliaPrep™ RNA Miniprep System Promega  Madison  WI  USA  based on the manufacturer's protocol.  The RNA quality of each sample was evaluated with a bioanalyzer  and only samples with an RNA Integrity Number RIN greater than 7.8 were selected for sequencing. Libraries were prepared following Novogene's in house protocol. Sequencing was carried out using paired end reads of 150 base pairs on an Illumina Novaseq 6000 Illumina  USA  yielding an average of 20 million reads per sample.,,pubmed:40373708,,RNA zebrafish larvae  control rep 1,GSM8695643,,source name:larvea|tissue:larvea|treatment:control|geo loc name:missing|collection date:missing,RNA zebrafish larvae  control rep 1,RAW reads were trimmed for Illumina adapter sequences using cutadapt version 1.18 and then aligned to the Danio rerio reference genome GRCz11 using STAR version 2.6.1c. Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample,larvea,,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,tissue:larvea|treatment:control,GSM8695643,GSM8695643: RNA zebrafish larvae  control rep 1; Danio rerio; RNA Seq,GSM8695643 r1,GSM8695643,1,RNA was isolated using the peqGold total RNA kit VWR Peqlab  Erlangen  Germany according to the manufacturer´s protocol. Novogene NGS DNA Library Prep Set Cat No.PT004. Libraries were sequenced onNovoSeq XPlus as indicated  Illumina.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq X Plus,,SRP552945,,,RNA_zebrafish_larvae_control_rep_1_R1.fq.gz RNA_zebrafish_larvae_control_rep_1_R2.fq.gz,fastq fastq,8152835100.0,27176117.0,GSM8695643 r1,0:150 1:150,A:2164487396;C:1922161762;G:1918935266;T:2142562884;N:4687792,150,150,,,2164487396,1922161762,1918935266,2142562884,4687792,SRX27151924,SRS23606409,SRA2123535,"Institute for Stem Cell Biology, RWTH Aachen University Medical School","Institute for Stem Cell Biology, RWTH Aachen University Medical School",,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,unknown,bulk,bulk,bulk,,Germany,2024-12-20,Larval,Larval,Undetermined,Undetermined
34564,SRR32105509,SRX27451088,SRS23877590,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,10ug 4,10ug 4,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:24|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,10ug 4,10ug 4,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,10ug-4.raw_1.fastq.gz 10ug-4.raw_2.fastq.gz,fastq fastq,6896050500.0,22986835.0,10ug 4.raw 1.fastq.gz,0:150 1:150,A:1748750850;C:1693354095;G:1732727536;T:1720741924;N:476095,150,150,,,1748750850,1693354095,1732727536,1720741924,476095,SRX27451088,SRS23877590,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34565,SRR32105510,SRX27451087,SRS23877587,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,10ug 3,10ug 3,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:23|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,10ug 3,10ug 3,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,10ug-3.raw_1.fastq.gz 10ug-3.raw_2.fastq.gz,fastq fastq,7963929300.0,26546431.0,10ug 3.raw 1.fastq.gz,0:150 1:150,A:2031952089;C:1946915859;G:1983760621;T:2000749958;N:550773,150,150,,,2031952089,1946915859,1983760621,2000749958,550773,SRX27451087,SRS23877587,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34566,SRR32105511,SRX27451086,SRS23877588,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,10ug 2,10ug 2,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:22|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,10ug 2,10ug 2,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,10ug-2.raw_1.fastq.gz 10ug-2.raw_2.fastq.gz,fastq fastq,7452654300.0,24842181.0,10ug 2.raw 1.fastq.gz,0:150 1:150,A:1893474820;C:1829930354;G:1868854325;T:1859881224;N:513577,150,150,,,1893474820,1829930354,1868854325,1859881224,513577,SRX27451086,SRS23877588,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34567,SRR32105512,SRX27451085,SRS23877585,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,10ug 1,10ug 1,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:21|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,10ug 1,10ug 1,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,10ug-1.raw_1.fastq.gz 10ug-1.raw_2.fastq.gz,fastq fastq,7062706200.0,23542354.0,10ug 1.raw 1.fastq.gz,0:150 1:150,A:1788073555;C:1735748492;G:1770878437;T:1767529804;N:475912,150,150,,,1788073555,1735748492,1770878437,1767529804,475912,SRX27451085,SRS23877585,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34569,SRR32105514,SRX27451083,SRS23877586,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,SC 4,SC 4,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:20|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,SC 4,SC 4,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,SC-4.raw_1.fastq.gz SC-4.raw_2.fastq.gz,fastq fastq,7301556000.0,24338520.0,SC 4.raw 1.fastq.gz,0:150 1:150,A:1856926170;C:1789274919;G:1829246096;T:1825603124;N:505691,150,150,,,1856926170,1789274919,1829246096,1825603124,505691,SRX27451083,SRS23877586,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34570,SRR32105515,SRX27451082,SRS23877584,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,SC 3,SC 3,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:19|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,SC 3,SC 3,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,SC-3.raw_1.fastq.gz SC-3.raw_2.fastq.gz,fastq fastq,7902209100.0,26340697.0,SC 3.raw 1.fastq.gz,0:150 1:150,A:2027055628;C:1918356291;G:1969072121;T:1987188644;N:536416,150,150,,,2027055628,1918356291,1969072121,1987188644,536416,SRX27451082,SRS23877584,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34571,SRR32105516,SRX27451081,SRS23877580,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,SC 2,SC 2,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:18|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,SC 2,SC 2,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,SC-2.raw_1.fastq.gz SC-2.raw_2.fastq.gz,fastq fastq,7695058200.0,25650194.0,SC 2.raw 1.fastq.gz,0:150 1:150,A:1957376969;C:1881709279;G:1921647145;T:1933783276;N:541531,150,150,,,1957376969,1881709279,1921647145,1933783276,541531,SRX27451081,SRS23877580,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
34572,SRR32105517,SRX27451080,SRS23877582,SRP559581,PRJNA1214993,Developmental toxicity of new psychoactive substance esketamine to zebrafish,PRJNA1214993,Other,New psychoactive substance esketamine has developmental toxicity and endocrine disrupting effects on zebrafish.,,,,SC 1,SC 1,,breed:not applicable|age:14 dpf|collection date:2024 11 15|geo loc name:China: Guangzhou|sex:not applicable|tissue:larva|order:17|BioSampleModel:Model organism or animal,,,,,,,,,Developmental toxicity of new psychoactive substance esketamine to zebrafish,SC 1,SC 1,larva,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP559581,,,SC-1.raw_1.fastq.gz SC-1.raw_2.fastq.gz,fastq fastq,6988861800.0,23296206.0,SC 1.raw 1.fastq.gz,0:150 1:150,A:1778524673;C:1708283935;G:1753402017;T:1748170625;N:480550,150,150,,,1778524673,1708283935,1753402017,1748170625,480550,SRX27451080,SRS23877582,SRA2059104,South China Normal University|School of Environment,South China Normal University,,,,,,,,,,,,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-01-24,Larval,Larval,Undetermined,Undetermined
35452,SRR32815440,SRX28098911,SRS24455832,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T4Danio rerio,,strain:T4|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T4|BioSampleModel:Model organism or animal,,,,,,,,,T4,T4,T4,T4,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T4_1.fq.gz T4_2.fq.gz,fastq fastq,6608651700.0,22028839.0,T4 1.fq.gz,0:150 1:150,A:1815401801;C:1489859310;G:1499379699;T:1804010890;N:0,150,150,,,1815401801,1489859310,1499379699,1804010890,0,SRX28098911,SRS24455832,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined
35453,SRR32815441,SRX28098910,SRS24455831,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T3Danio rerio,,strain:T3|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T3|BioSampleModel:Model organism or animal,,,,,,,,,T3,T3,T3,T3,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T3_1.fq.gz T3_2.fq.gz,fastq fastq,6656167200.0,22187224.0,T3 1.fq.gz,0:150 1:150,A:1840552276;C:1489247530;G:1499297584;T:1827069810;N:0,150,150,,,1840552276,1489247530,1499297584,1827069810,0,SRX28098910,SRS24455831,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined
35454,SRR32815442,SRX28098909,SRS24455830,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T2Danio rerio,,strain:T2|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T2|BioSampleModel:Model organism or animal,,,,,,,,,T2,T2,T2,T2,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T2_1.fq.gz T2_2.fq.gz,fastq fastq,6622204800.0,22074016.0,T2 1.fq.gz,0:150 1:150,A:1834396150;C:1480094606;G:1490046882;T:1817667162;N:0,150,150,,,1834396150,1480094606,1490046882,1817667162,0,SRX28098909,SRS24455830,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined
35455,SRR32815443,SRX28098908,SRS24455829,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,T1Danio rerio,,strain:T1|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:T1|BioSampleModel:Model organism or animal,,,,,,,,,T1,T1,T1,T1,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,T1_1.fq.gz T1_2.fq.gz,fastq fastq,6626122500.0,22087075.0,T1 1.fq.gz,0:150 1:150,A:1833541012;C:1481665295;G:1491851279;T:1819064914;N:0,150,150,,,1833541012,1481665295,1491851279,1819064914,0,SRX28098908,SRS24455829,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined
35456,SRR32815444,SRX28098907,SRS24455828,SRP572346,PRJNA1240620,The mechanism of maternal inheritance of glycolipid metabolism disorder in a zebrafish model of type 2 diabetes,PRJNA1240620,Other,,,,,,Q4Danio rerio,,strain:Q4|age:96hpf|collection date:2023 12 20|geo loc name:China: Xiangyang|sex:missing|tissue:Tissue of juvenile fish|replicate:Q4|BioSampleModel:Model organism or animal,,,,,,,,,Q4,Q4,Q4,Q4,,,RNA-Seq,METATRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP572346,,,Q4_1.fq.gz Q4_2.fq.gz,fastq fastq,6646083600.0,22153612.0,Q4 1.fq.gz,0:150 1:150,A:1823086981;C:1499930776;G:1510718905;T:1812346938;N:0,150,150,,,1823086981,1499930776,1510718905,1812346938,0,SRX28098907,SRS24455828,SRA2098321,Wuhan University of Science and Technology|School of Medicine,Wuhan University of Science and Technology,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2025-03-22,Larval,Larval,Undetermined,Undetermined