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 68685,SRR18173220,SRX14320215,SRS12136321,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 48hpf Replicate 4,GSM5924083,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control,Control 48hpf Replicate 4,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:Control,GSM5924083,GSM5924083: Control 48hpf Replicate 4; Danio rerio; RNA Seq,GSM5924083 r1,GSM5924083,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_48hpf_4_2.fq.gz Control_48hpf_4_1.fq.gz,fastq fastq,4893304000.0,48933040.0,GSM5924083 r1,0:100 1:100,A:1295107147;C:1131453899;G:1158231463;T:1307269653;N:1241838,100,100,,,1295107147,1131453899,1158231463,1307269653,1241838,SRX14320215,SRS12136321,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94011,,0.0801,,0.6927,,0.48073,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68686,SRR18173221,SRX14320214,SRS12136320,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 48hpf Replicate 3,GSM5924082,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control,Control 48hpf Replicate 3,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:Control,GSM5924082,GSM5924082: Control 48hpf Replicate 3; Danio rerio; RNA Seq,GSM5924082 r1,GSM5924082,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_48hpf_3_1.fq.gz Control_48hpf_3_2.fq.gz,fastq fastq,4673710400.0,46737104.0,GSM5924082 r1,0:100 1:100,A:1239135128;C:1079263067;G:1106439223;T:1248694558;N:178424,100,100,,,1239135128,1079263067,1106439223,1248694558,178424,SRX14320214,SRS12136320,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9388,,0.09027,,0.6896,,0.47121,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68687,SRR18173222,SRX14320213,SRS12136319,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 48hpf Replicate 2,GSM5924081,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control,Control 48hpf Replicate 2,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:Control,GSM5924081,GSM5924081: Control 48hpf Replicate 2; Danio rerio; RNA Seq,GSM5924081 r1,GSM5924081,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_48hpf_2_2.fq.gz Control_48hpf_2_1.fq.gz,fastq fastq,4669056600.0,46690566.0,GSM5924081 r1,0:100 1:100,A:1230949768;C:1083419632;G:1111527320;T:1243051944;N:107936,100,100,,,1230949768,1083419632,1111527320,1243051944,107936,SRX14320213,SRS12136319,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94517,,0.08072,,0.70084,,0.47423,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68688,SRR18173223,SRX14320212,SRS12136318,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 48hpf Replicate 1,GSM5924080,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:Control,Control 48hpf Replicate 1,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:Control,GSM5924080,GSM5924080: Control 48hpf Replicate 1; Danio rerio; RNA Seq,GSM5924080 r1,GSM5924080,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_48hpf_1_2.fq.gz Control_48hpf_1_1.fq.gz,fastq fastq,4710239800.0,47102398.0,GSM5924080 r1,0:100 1:100,A:1244163615;C:1092143032;G:1118126753;T:1255696249;N:110151,100,100,,,1244163615,1092143032,1118126753,1255696249,110151,SRX14320212,SRS12136318,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94203,,0.08895,,0.69335,,0.46922,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68689,SRR18173224,SRX14320211,SRS12136317,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 120hpf Replicate 4,GSM5924079,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:Control,Control 120hpf Replicate 4,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:Control,GSM5924079,GSM5924079: Control 120hpf Replicate 4; Danio rerio; RNA Seq,GSM5924079 r1,GSM5924079,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_120hpf_4_2.fq.gz Control_120hpf_4_1.fq.gz,fastq fastq,4923254200.0,49232542.0,GSM5924079 r1,0:100 1:100,A:1318267566;C:1124031311;G:1150556519;T:1329162427;N:1236377,100,100,,,1318267566,1124031311,1150556519,1329162427,1236377,SRX14320211,SRS12136317,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92741,,0.09968,,0.67286,,0.48229,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68690,SRR18173225,SRX14320210,SRS12136316,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 120hpf Replicate 3,GSM5924078,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:Control,Control 120hpf Replicate 3,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:Control,GSM5924078,GSM5924078: Control 120hpf Replicate 3; Danio rerio; RNA Seq,GSM5924078 r1,GSM5924078,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_120hpf_3_1.fq.gz Control_120hpf_3_2.fq.gz,fastq fastq,4647840800.0,46478408.0,GSM5924078 r1,0:100 1:100,A:1247522602;C:1057954537;G:1083169525;T:1258914406;N:279730,100,100,,,1247522602,1057954537,1083169525,1258914406,279730,SRX14320210,SRS12136316,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93152,,0.09996,,0.67006,,0.48366,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68691,SRR18173226,SRX14320209,SRS12136315,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 120hpf Replicate 2,GSM5924077,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:Control,Control 120hpf Replicate 2,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:Control,GSM5924077,GSM5924077: Control 120hpf Replicate 2; Danio rerio; RNA Seq,GSM5924077 r1,GSM5924077,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_120hpf_2_1.fq.gz Control_120hpf_2_2.fq.gz,fastq fastq,4642376000.0,46423760.0,GSM5924077 r1,0:100 1:100,A:1234820091;C:1067250899;G:1094463424;T:1245738190;N:103396,100,100,,,1234820091,1067250899,1094463424,1245738190,103396,SRX14320209,SRS12136315,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93467,,0.09742,,0.6662,,0.46932,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68692,SRR18173227,SRX14320208,SRS12136314,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,Control 120hpf Replicate 1,GSM5924076,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:Control,Control 120hpf Replicate 1,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:Control,GSM5924076,GSM5924076: Control 120hpf Replicate 1; Danio rerio; RNA Seq,GSM5924076 r1,GSM5924076,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,Control_120hpf_1_2.fq.gz Control_120hpf_1_1.fq.gz,fastq fastq,4680845400.0,46808454.0,GSM5924076 r1,0:100 1:100,A:1249629460;C:1071123930;G:1100499112;T:1259432753;N:160145,100,100,,,1249629460,1071123930,1100499112,1259432753,160145,SRX14320208,SRS12136314,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93102,,0.11394,,0.66608,,0.48681,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68693,SRR18173228,SRX14320207,SRS12136313,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 48hpf Replicate 4,GSM5924075,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G,5G 48hpf Replicate 4,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:5G,GSM5924075,GSM5924075: 5G 48hpf Replicate 4; Danio rerio; RNA Seq,GSM5924075 r1,GSM5924075,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_48hpf_4_2.fq.gz 5G_48hpf_4_1.fq.gz,fastq fastq,3960397600.0,39603976.0,GSM5924075 r1,0:100 1:100,A:1055375851;C:908722788;G:931610403;T:1063707959;N:980599,100,100,,,1055375851,908722788,931610403,1063707959,980599,SRX14320207,SRS12136313,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93498,,0.09353,,0.6884,,0.48205,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68694,SRR18173229,SRX14320206,SRS12136312,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 48hpf Replicate 3,GSM5924074,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G,5G 48hpf Replicate 3,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:5G,GSM5924074,GSM5924074: 5G 48hpf Replicate 3; Danio rerio; RNA Seq,GSM5924074 r1,GSM5924074,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_48hpf_3_1.fq.gz 5G_48hpf_3_2.fq.gz,fastq fastq,4666094000.0,46660940.0,GSM5924074 r1,0:100 1:100,A:1237561088;C:1075964364;G:1103985038;T:1248326386;N:257124,100,100,,,1237561088,1075964364,1103985038,1248326386,257124,SRX14320206,SRS12136312,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93689,,0.09226,,0.68655,,0.46431,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68695,SRR18173230,SRX14320205,SRS12136311,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 48hpf Replicate 2,GSM5924073,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G,5G 48hpf Replicate 2,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:5G,GSM5924073,GSM5924073: 5G 48hpf Replicate 2; Danio rerio; RNA Seq,GSM5924073 r1,GSM5924073,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_48hpf_2_1.fq.gz 5G_48hpf_2_2.fq.gz,fastq fastq,4687152000.0,46871520.0,GSM5924073 r1,0:100 1:100,A:1241838266;C:1082317123;G:1110355516;T:1252466907;N:174188,100,100,,,1241838266,1082317123,1110355516,1252466907,174188,SRX14320205,SRS12136311,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94454,,0.08717,,0.69122,,0.47277,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68696,SRR18173231,SRX14320204,SRS12136310,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 48hpf Replicate 1,GSM5924072,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:48 hpf|treatment:5G,5G 48hpf Replicate 1,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:48 hpf|treatment:5G,GSM5924072,GSM5924072: 5G 48hpf Replicate 1; Danio rerio; RNA Seq,GSM5924072 r1,GSM5924072,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_48hpf_1_1.fq.gz 5G_48hpf_1_2.fq.gz,fastq fastq,4703041000.0,47030410.0,GSM5924072 r1,0:100 1:100,A:1245130239;C:1085229448;G:1115856477;T:1256653090;N:171746,100,100,,,1245130239,1085229448,1115856477,1256653090,171746,SRX14320204,SRS12136310,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94571,,0.0868,,0.69798,,0.47971,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Hatching,Embryo,Whole Organism,All anatomical structures 68697,SRR18173232,SRX14320203,SRS12136309,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 120hpf Replicate 4,GSM5924071,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:5G,5G 120hpf Replicate 4,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:5G,GSM5924071,GSM5924071: 5G 120hpf Replicate 4; Danio rerio; RNA Seq,GSM5924071 r1,GSM5924071,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_120hpf_4_1.fq.gz 5G_120hpf_4_2.fq.gz,fastq fastq,4715030400.0,47150304.0,GSM5924071 r1,0:100 1:100,A:1261218112;C:1077110080;G:1103389780;T:1272133362;N:1179066,100,100,,,1261218112,1077110080,1103389780,1272133362,1179066,SRX14320203,SRS12136309,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9275,,0.10307,,0.67083,,0.47242,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68698,SRR18173233,SRX14320202,SRS12136308,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 120hpf Replicate 3,GSM5924070,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:5G,5G 120hpf Replicate 3,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:5G,GSM5924070,GSM5924070: 5G 120hpf Replicate 3; Danio rerio; RNA Seq,GSM5924070 r1,GSM5924070,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_120hpf_3_1.fq.gz 5G_120hpf_3_2.fq.gz,fastq fastq,4656738600.0,46567386.0,GSM5924070 r1,0:100 1:100,A:1248651666;C:1060616489;G:1087008602;T:1260285546;N:176297,100,100,,,1248651666,1060616489,1087008602,1260285546,176297,SRX14320202,SRS12136308,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93209,,0.09986,,0.66314,,0.48434,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68699,SRR18173234,SRX14320201,SRS12136307,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 120hpf Replicate 2,GSM5924069,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:5G,5G 120hpf Replicate 2,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:5G,GSM5924069,GSM5924069: 5G 120hpf Replicate 2; Danio rerio; RNA Seq,GSM5924069 r1,GSM5924069,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_120hpf_2_1.fq.gz 5G_120hpf_2_2.fq.gz,fastq fastq,4646546600.0,46465466.0,GSM5924069 r1,0:100 1:100,A:1238225585;C:1067169010;G:1093116587;T:1247937654;N:97764,100,100,,,1238225585,1067169010,1093116587,1247937654,97764,SRX14320201,SRS12136307,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93211,,0.10594,,0.67014,,0.47987,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 68700,SRR18173235,SRX14320200,SRS12136306,SRP361858,PRJNA811237,Transcriptomic and long term behavioral deficits associated with developmental 3.5 GHz radiofrequency radiation exposures in zebrafish,GSE197627,Transcriptome Analysis,"Transcriptomic data for 48 hpf and 120 hpf zebrafish embryos developmentally exposed to 3.5 GHz of radiofrequency radiation. Overall design: Two treatments Controls and RFR exposed referred to as ""5G"". Controls were exposed to no radiation. RFR exposed were exposed ttwo xxx.5 GHz 30 dBm radiation from 6 hpf 48 hpf. Embryos collected at 48 hpf and 120 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.",,pubmed:35434172,,5G 120hpf Replicate 1,GSM5924068,,source name:Zebrafish embryonic total RNA|tissue:whole embryos|developmental stage:120 hpf|treatment:5G,5G 120hpf Replicate 1,SOAPnuke for read filter. HISAT2 for genome mapping. Bowtie2 for reference genome map. DESeq2 for differential expression. Genome build: GCF 000002035.6 GRCz11 Supplementary files format and content: Excel files with compiled normalized count and clean read files for all samples. Supplementary files format and content: AllSamples.GeneExpression.FPKM.xlsx: FPKM normalized read counts. Supplementary files format and content: FilterSummary.xlsx: Read percentages. Supplementary files format and content: GeneExpressionSummary.xlsx: Clean read and mapping %.,Zebrafish embryonic total RNA,Zebrafish embryos were untreated or treated with 3.5 GHz RFR from 6 hpf 48 hpf.,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,tissue:whole embryos|developmental stage:120 hpf|treatment:5G,GSM5924068,GSM5924068: 5G 120hpf Replicate 1; Danio rerio; RNA Seq,GSM5924068 r1,GSM5924068,1,Total RNA was isolated from zebrafish embryos at 48 hpf and 120 hpf. Library prep and sequencing were done on a Beijing Genomics Institute DNBseq G50 platform with 100 bl PE.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP361858,,,5G_120hpf_1_1.fq.gz 5G_120hpf_1_2.fq.gz,fastq fastq,4681798400.0,46817984.0,GSM5924068 r1,0:100 1:100,A:1253713297;C:1068488584;G:1095439488;T:1263988713;N:168318,100,100,,,1253713297,1068488584,1095439488,1263988713,168318,SRX14320200,SRS12136306,SRA1379040,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93351,,0.1075,,0.66553,,0.4777,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-02-28,Larval,Larval,Whole Organism,All anatomical structures 69994,SRR19264376,SRX15324808,SRS13053424,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 50 µM Replicate 4,GSM6165409,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA Retene 50 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165409,GSM6165409: RNA Retene 50 µM Replicate 4; Danio rerio; RNA Seq,GSM6165409 r1,GSM6165409,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret32_2.fq Ret32_1.fq,fastq fastq,4572659600.0,45726596.0,GSM6165409 r1,0:100 1:100,A:1232170294;C:1035171387;G:1089126986;T:1216190933;N:0,100,100,,,1232170294,1035171387,1089126986,1216190933,0,SRX15324808,SRS13053424,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.91127,,0.11591,,0.71317,,0.48482,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 69995,SRR19264377,SRX15324807,SRS13053423,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 50 µM Replicate 3,GSM6165408,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA Retene 50 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165408,GSM6165408: RNA Retene 50 µM Replicate 3; Danio rerio; RNA Seq,GSM6165408 r1,GSM6165408,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret31_1.fq Ret31_2.fq,fastq fastq,4579737600.0,45797376.0,GSM6165408 r1,0:100 1:100,A:1219008458;C:1049195671;G:1093502477;T:1218030994;N:0,100,100,,,1219008458,1049195671,1093502477,1218030994,0,SRX15324807,SRS13053423,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93002,,0.08752,,0.7094,,0.493,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 69996,SRR19264378,SRX15324806,SRS13053422,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 50 µM Replicate 2,GSM6165407,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA Retene 50 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165407,GSM6165407: RNA Retene 50 µM Replicate 2; Danio rerio; RNA Seq,GSM6165407 r1,GSM6165407,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret30_1.fq Ret30_2.fq,fastq fastq,4590395200.0,45903952.0,GSM6165407 r1,0:100 1:100,A:1207114959;C:1061518436;G:1113201421;T:1208560384;N:0,100,100,,,1207114959,1061518436,1113201421,1208560384,0,SRX15324806,SRS13053422,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93837,,0.08052,,0.70542,,0.49074,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 69997,SRR19264379,SRX15324805,SRS13053421,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 50 µM Replicate 1,GSM6165406,,tissue:Whole zebrafish larvae|timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,RNA Retene 50 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 50 µM|FISH strain:Tropical 5D,GSM6165406,GSM6165406: RNA Retene 50 µM Replicate 1; Danio rerio; RNA Seq,GSM6165406 r1,GSM6165406,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret29_2.fq Ret29_1.fq,fastq fastq,4565893800.0,45658938.0,GSM6165406 r1,0:100 1:100,A:1216518504;C:1041975840;G:1092350073;T:1215049383;N:0,100,100,,,1216518504,1041975840,1092350073,1215049383,0,SRX15324805,SRS13053421,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93015,,0.0903,,0.71088,,0.49418,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 69998,SRR19264380,SRX15324804,SRS13053420,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 20 µM Replicate 4,GSM6165405,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA Retene 20 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165405,GSM6165405: RNA Retene 20 µM Replicate 4; Danio rerio; RNA Seq,GSM6165405 r1,GSM6165405,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret28_2.fq Ret28_1.fq,fastq fastq,4605153200.0,46051532.0,GSM6165405 r1,0:100 1:100,A:1237345826;C:1045225477;G:1091001207;T:1231580690;N:0,100,100,,,1237345826,1045225477,1091001207,1231580690,0,SRX15324804,SRS13053420,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92128,,0.10244,,0.70524,,0.49879,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 69999,SRR19264381,SRX15324803,SRS13053419,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 20 µM Replicate 3,GSM6165404,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA Retene 20 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165404,GSM6165404: RNA Retene 20 µM Replicate 3; Danio rerio; RNA Seq,GSM6165404 r1,GSM6165404,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret27_2.fq Ret27_1.fq,fastq fastq,4596933800.0,45969338.0,GSM6165404 r1,0:100 1:100,A:1227576643;C:1047500037;G:1096955088;T:1224902032;N:0,100,100,,,1227576643,1047500037,1096955088,1224902032,0,SRX15324803,SRS13053419,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92878,,0.09222,,0.70544,,0.49805,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70000,SRR19264382,SRX15324802,SRS13053418,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 20 µM Replicate 2,GSM6165403,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA Retene 20 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165403,GSM6165403: RNA Retene 20 µM Replicate 2; Danio rerio; RNA Seq,GSM6165403 r1,GSM6165403,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret26_1.fq Ret26_2.fq,fastq fastq,4596114400.0,45961144.0,GSM6165403 r1,0:100 1:100,A:1220023927;C:1054918236;G:1104509767;T:1216662470;N:0,100,100,,,1220023927,1054918236,1104509767,1216662470,0,SRX15324802,SRS13053418,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92714,,0.08942,,0.70834,,0.48781,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70001,SRR19264383,SRX15324801,SRS13053417,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 20 µM Replicate 1,GSM6165402,,tissue:Whole zebrafish larvae|timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,RNA Retene 20 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 20 µM|FISH strain:Tropical 5D,GSM6165402,GSM6165402: RNA Retene 20 µM Replicate 1; Danio rerio; RNA Seq,GSM6165402 r1,GSM6165402,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret25_1.fq Ret25_2.fq,fastq fastq,4588797000.0,45887970.0,GSM6165402 r1,0:100 1:100,A:1221596882;C:1049586741;G:1105734392;T:1211878985;N:0,100,100,,,1221596882,1049586741,1105734392,1211878985,0,SRX15324801,SRS13053417,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92083,,0.08963,,0.70936,,0.48202,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70002,SRR19264384,SRX15324800,SRS13053416,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 8 µM Replicate 4,GSM6165401,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA Retene 8 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165401,GSM6165401: RNA Retene 8 µM Replicate 4; Danio rerio; RNA Seq,GSM6165401 r1,GSM6165401,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret24_1.fq Ret24_2.fq,fastq fastq,4624156600.0,46241566.0,GSM6165401 r1,0:100 1:100,A:1205935971;C:1080155692;G:1125498382;T:1212566555;N:0,100,100,,,1205935971,1080155692,1125498382,1212566555,0,SRX15324800,SRS13053416,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94086,,0.0771,,0.70076,,0.48339,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70003,SRR19264385,SRX15324799,SRS13053415,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 8 µM Replicate 3,GSM6165400,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA Retene 8 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165400,GSM6165400: RNA Retene 8 µM Replicate 3; Danio rerio; RNA Seq,GSM6165400 r1,GSM6165400,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret23_1.fq Ret23_2.fq,fastq fastq,4624324200.0,46243242.0,GSM6165400 r1,0:100 1:100,A:1218844152;C:1067729229;G:1115817781;T:1221933038;N:0,100,100,,,1218844152,1067729229,1115817781,1221933038,0,SRX15324799,SRS13053415,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93497,,0.07979,,0.70916,,0.49162,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70004,SRR19264386,SRX15324798,SRS13053414,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 8 µM Replicate 2,GSM6165399,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA Retene 8 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165399,GSM6165399: RNA Retene 8 µM Replicate 2; Danio rerio; RNA Seq,GSM6165399 r1,GSM6165399,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret22_1.fq Ret22_2.fq,fastq fastq,4630355600.0,46303556.0,GSM6165399 r1,0:100 1:100,A:1234125157;C:1058827735;G:1103596542;T:1233806166;N:0,100,100,,,1234125157,1058827735,1103596542,1233806166,0,SRX15324798,SRS13053414,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92491,,0.09055,,0.71267,,0.49637,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70005,SRR19264387,SRX15324797,SRS13053413,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 8 µM Replicate 1,GSM6165398,,tissue:Whole zebrafish larvae|timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,RNA Retene 8 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 8 µM|FISH strain:Tropical 5D,GSM6165398,GSM6165398: RNA Retene 8 µM Replicate 1; Danio rerio; RNA Seq,GSM6165398 r1,GSM6165398,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret21_1.fq Ret21_2.fq,fastq fastq,4386431000.0,43864310.0,GSM6165398 r1,0:100 1:100,A:1164169162;C:1006840682;G:1048654370;T:1166766786;N:0,100,100,,,1164169162,1006840682,1048654370,1166766786,0,SRX15324797,SRS13053413,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93229,,0.08542,,0.71236,,0.49127,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70006,SRR19264388,SRX15324796,SRS13053412,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 3.2 µM Replicate 4,GSM6165397,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA Retene 3.2 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165397,GSM6165397: RNA Retene 3.2 µM Replicate 4; Danio rerio; RNA Seq,GSM6165397 r1,GSM6165397,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret20_1.fq Ret20_2.fq,fastq fastq,4383419800.0,43834198.0,GSM6165397 r1,0:100 1:100,A:1156733640;C:1010925303;G:1051454425;T:1164306432;N:0,100,100,,,1156733640,1010925303,1051454425,1164306432,0,SRX15324796,SRS13053412,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93759,,0.0801,,0.70879,,0.49551,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70007,SRR19264389,SRX15324795,SRS13053411,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 3.2 µM Replicate 3,GSM6165396,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA Retene 3.2 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165396,GSM6165396: RNA Retene 3.2 µM Replicate 3; Danio rerio; RNA Seq,GSM6165396 r1,GSM6165396,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret19_2.fq Ret19_1.fq,fastq fastq,4389521800.0,43895218.0,GSM6165396 r1,0:100 1:100,A:1162594360;C:1009534036;G:1049443810;T:1167949594;N:0,100,100,,,1162594360,1009534036,1049443810,1167949594,0,SRX15324795,SRS13053411,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93573,,0.08567,,0.70611,,0.48715,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70008,SRR19264390,SRX15324794,SRS13053410,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 3.2 µM Replicate 2,GSM6165395,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA Retene 3.2 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165395,GSM6165395: RNA Retene 3.2 µM Replicate 2; Danio rerio; RNA Seq,GSM6165395 r1,GSM6165395,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret18_1.fq Ret18_2.fq,fastq fastq,4397887000.0,43978870.0,GSM6165395 r1,0:100 1:100,A:1163596419;C:1012807954;G:1054042174;T:1167440453;N:0,100,100,,,1163596419,1012807954,1054042174,1167440453,0,SRX15324794,SRS13053410,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9311,,0.09135,,0.70518,,0.49131,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70009,SRR19264391,SRX15324793,SRS13053409,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 3.2 µM Replicate 1,GSM6165394,,tissue:Whole zebrafish larvae|timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,RNA Retene 3.2 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 3.2 µM|FISH strain:Tropical 5D,GSM6165394,GSM6165394: RNA Retene 3.2 µM Replicate 1; Danio rerio; RNA Seq,GSM6165394 r1,GSM6165394,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret17_1.fq Ret17_2.fq,fastq fastq,4615185200.0,46151852.0,GSM6165394 r1,0:100 1:100,A:1209825639;C:1071817166;G:1115963072;T:1217579323;N:0,100,100,,,1209825639,1071817166,1115963072,1217579323,0,SRX15324793,SRS13053409,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.94207,,0.07533,,0.70672,,0.49039,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70010,SRR19264392,SRX15324792,SRS13053408,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 1.28 µM Replicate 4,GSM6165393,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA Retene 1.28 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165393,GSM6165393: RNA Retene 1.28 µM Replicate 4; Danio rerio; RNA Seq,GSM6165393 r1,GSM6165393,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret16_1.fq Ret16_2.fq,fastq fastq,4384911400.0,43849114.0,GSM6165393 r1,0:100 1:100,A:1170400515;C:1001704172;G:1042001905;T:1170804808;N:0,100,100,,,1170400515,1001704172,1042001905,1170804808,0,SRX15324792,SRS13053408,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92473,,0.09931,,0.70721,,0.48941,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70011,SRR19264393,SRX15324791,SRS13053407,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 1.28 µM Replicate 3,GSM6165392,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA Retene 1.28 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165392,GSM6165392: RNA Retene 1.28 µM Replicate 3; Danio rerio; RNA Seq,GSM6165392 r1,GSM6165392,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret15_1.fq Ret15_2.fq,fastq fastq,4384128000.0,43841280.0,GSM6165392 r1,0:100 1:100,A:1175348660;C:998065234;G:1039750478;T:1170963628;N:0,100,100,,,1175348660,998065234,1039750478,1170963628,0,SRX15324791,SRS13053407,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92006,,0.10061,,0.71029,,0.49305,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70012,SRR19264394,SRX15324790,SRS13053406,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 1.28 µM Replicate 2,GSM6165391,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA Retene 1.28 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165391,GSM6165391: RNA Retene 1.28 µM Replicate 2; Danio rerio; RNA Seq,GSM6165391 r1,GSM6165391,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret14_1.fq Ret14_2.fq,fastq fastq,4386590600.0,43865906.0,GSM6165391 r1,0:100 1:100,A:1162629143;C:1008431955;G:1048944378;T:1166585124;N:0,100,100,,,1162629143,1008431955,1048944378,1166585124,0,SRX15324790,SRS13053406,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92918,,0.09061,,0.70615,,0.48926,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70013,SRR19264395,SRX15324789,SRS13053405,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 1.28 µM Replicate 1,GSM6165390,,tissue:Whole zebrafish larvae|timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,RNA Retene 1.28 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 1.28 µM|FISH strain:Tropical 5D,GSM6165390,GSM6165390: RNA Retene 1.28 µM Replicate 1; Danio rerio; RNA Seq,GSM6165390 r1,GSM6165390,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret13_1.fq Ret13_2.fq,fastq fastq,4630946000.0,46309460.0,GSM6165390 r1,0:100 1:100,A:1222553747;C:1068043014;G:1111862124;T:1228487115;N:0,100,100,,,1222553747,1068043014,1111862124,1228487115,0,SRX15324789,SRS13053405,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9355,,0.08198,,0.71096,,0.49274,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70014,SRR19264396,SRX15324788,SRS13053404,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.512 µM Replicate 4,GSM6165389,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA Retene 0.512 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165389,GSM6165389: RNA Retene 0.512 µM Replicate 4; Danio rerio; RNA Seq,GSM6165389 r1,GSM6165389,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret12_1.fq Ret12_2.fq,fastq fastq,4597887800.0,45978878.0,GSM6165389 r1,0:100 1:100,A:1211629239;C:1061362233;G:1107475120;T:1217421208;N:0,100,100,,,1211629239,1061362233,1107475120,1217421208,0,SRX15324788,SRS13053404,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93986,,0.07927,,0.70907,,0.47669,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70015,SRR19264397,SRX15324787,SRS13053403,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.512 µM Replicate 3,GSM6165388,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA Retene 0.512 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165388,GSM6165388: RNA Retene 0.512 µM Replicate 3; Danio rerio; RNA Seq,GSM6165388 r1,GSM6165388,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret11_1.fq Ret11_2.fq,fastq fastq,4560391600.0,45603916.0,GSM6165388 r1,0:100 1:100,A:1204481849;C:1049709181;G:1091882975;T:1214317595;N:0,100,100,,,1204481849,1049709181,1091882975,1214317595,0,SRX15324787,SRS13053403,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93399,,0.0879,,0.70617,,0.48281,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70016,SRR19264398,SRX15324786,SRS13053402,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.512 µM Replicate 2,GSM6165387,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA Retene 0.512 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165387,GSM6165387: RNA Retene 0.512 µM Replicate 2; Danio rerio; RNA Seq,GSM6165387 r1,GSM6165387,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret10_2.fq Ret10_1.fq,fastq fastq,4542900600.0,45429006.0,GSM6165387 r1,0:100 1:100,A:1189304147;C:1055343156;G:1099652770;T:1198600527;N:0,100,100,,,1189304147,1055343156,1099652770,1198600527,0,SRX15324786,SRS13053402,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.93819,,0.07628,,0.712,,0.4832,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70017,SRR19264399,SRX15324785,SRS13053401,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.512 µM Replicate 1,GSM6165386,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,RNA Retene 0.512 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.512 µM|FISH strain:Tropical 5D,GSM6165386,GSM6165386: RNA Retene 0.512 µM Replicate 1; Danio rerio; RNA Seq,GSM6165386 r1,GSM6165386,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret9_1.fq Ret9_2.fq,fastq fastq,4554791000.0,45547910.0,GSM6165386 r1,0:100 1:100,A:1208091587;C:1047925998;G:1085454060;T:1213319355;N:0,100,100,,,1208091587,1047925998,1085454060,1213319355,0,SRX15324785,SRS13053401,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92696,,0.08964,,0.70725,,0.47678,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70018,SRR19264400,SRX15324784,SRS13053400,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.205 µM Replicate 4,GSM6165385,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA Retene 0.205 µM Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165385,GSM6165385: RNA Retene 0.205 µM Replicate 4; Danio rerio; RNA Seq,GSM6165385 r1,GSM6165385,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret8_1.fq Ret8_2.fq,fastq fastq,4790224600.0,47902246.0,GSM6165385 r1,0:100 1:100,A:1284827524;C:1090358436;G:1135298341;T:1279740299;N:0,100,100,,,1284827524,1090358436,1135298341,1279740299,0,SRX15324784,SRS13053400,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.91468,,0.10225,,0.70688,,0.48401,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70019,SRR19264401,SRX15324783,SRS13053399,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.205 µM Replicate 3,GSM6165384,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA Retene 0.205 µM Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165384,GSM6165384: RNA Retene 0.205 µM Replicate 3; Danio rerio; RNA Seq,GSM6165384 r1,GSM6165384,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret7_1.fq Ret7_2.fq,fastq fastq,4549850800.0,45498508.0,GSM6165384 r1,0:100 1:100,A:1208192098;C:1046598883;G:1088752462;T:1206307357;N:0,100,100,,,1208192098,1046598883,1088752462,1206307357,0,SRX15324783,SRS13053399,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92485,,0.08773,,0.71482,,0.4865,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70020,SRR19264402,SRX15324782,SRS13053398,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.205 µM Replicate 2,GSM6165383,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA Retene 0.205 µM Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165383,GSM6165383: RNA Retene 0.205 µM Replicate 2; Danio rerio; RNA Seq,GSM6165383 r1,GSM6165383,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret6_1.fq Ret6_2.fq,fastq fastq,4537342000.0,45373420.0,GSM6165383 r1,0:100 1:100,A:1199051958;C:1046776379;G:1091726768;T:1199786895;N:0,100,100,,,1199051958,1046776379,1091726768,1199786895,0,SRX15324782,SRS13053398,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92685,,0.08488,,0.70946,,0.4809,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70021,SRR19264403,SRX15324781,SRS13053397,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Retene 0.205 µM Replicate 1,GSM6165382,,tissue:Whole zebrafish larvae|timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,RNA Retene 0.205 µM Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf 0.205 µM|FISH strain:Tropical 5D,GSM6165382,GSM6165382: RNA Retene 0.205 µM Replicate 1; Danio rerio; RNA Seq,GSM6165382 r1,GSM6165382,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret5_1.fq Ret5_2.fq,fastq fastq,4567176000.0,45671760.0,GSM6165382 r1,0:100 1:100,A:1207574600;C:1052993527;G:1095598503;T:1211009370;N:0,100,100,,,1207574600,1052993527,1095598503,1211009370,0,SRX15324781,SRS13053397,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92733,,0.08445,,0.7083,,0.47655,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70022,SRR19264404,SRX15324780,SRS13053396,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Vehicle control Replicate 4,GSM6165381,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA Vehicle control Replicate 4,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165381,GSM6165381: RNA Vehicle control Replicate 4; Danio rerio; RNA Seq,GSM6165381 r1,GSM6165381,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret4_1.fq Ret4_2.fq,fastq fastq,4553955200.0,45539552.0,GSM6165381 r1,0:100 1:100,A:1202023760;C:1052394121;G:1091476117;T:1208061202;N:0,100,100,,,1202023760,1052394121,1091476117,1208061202,0,SRX15324780,SRS13053396,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92839,,0.0842,,0.70812,,0.48512,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70023,SRR19264405,SRX15324779,SRS13053395,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Vehicle control Replicate 3,GSM6165380,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA Vehicle control Replicate 3,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165380,GSM6165380: RNA Vehicle control Replicate 3; Danio rerio; RNA Seq,GSM6165380 r1,GSM6165380,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret3_1.fq Ret3_2.fq,fastq fastq,4786982600.0,47869826.0,GSM6165380 r1,0:100 1:100,A:1260496096;C:1108347336;G:1153576121;T:1264563047;N:0,100,100,,,1260496096,1108347336,1153576121,1264563047,0,SRX15324779,SRS13053395,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9294,,0.08138,,0.71045,,0.47542,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70024,SRR19264406,SRX15324778,SRS13053394,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Vehicle control Replicate 2,GSM6165379,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA Vehicle control Replicate 2,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165379,GSM6165379: RNA Vehicle control Replicate 2; Danio rerio; RNA Seq,GSM6165379 r1,GSM6165379,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret2_1.fq Ret2_2.fq,fastq fastq,4546668600.0,45466686.0,GSM6165379 r1,0:100 1:100,A:1203655800;C:1046900520;G:1091124255;T:1204988025;N:0,100,100,,,1203655800,1046900520,1091124255,1204988025,0,SRX15324778,SRS13053394,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.92452,,0.09064,,0.69796,,0.46741,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70025,SRR19264407,SRX15324777,SRS13053393,SRP375841,PRJNA839281,Concentration response gene expression analysis in zebrafish reveals phenotypically anchored transcriptional responses to retene,GSE203258,Transcriptome Analysis,Purpose: Assess transcriptomic changes in response to phenotypically anchored retene concentrations. By combining data from all concentrations we inferred a gene co expression network highlighting key transcripts and modules important to toxicity response to retene. Overall design: Transcriptomic profiles of 48 hpf zebrafish,,,,RNA Vehicle control Replicate 1,GSM6165378,,tissue:Whole zebrafish larvae|timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,RNA Vehicle control Replicate 1,Reads were aligned to the GRCz11 genome using the Star Aligner Reads were counted using HTSeq with an alignment valud cutoff of a10 using the gff file for the GRCz11 genome Raw counts were normalized using DESeq2 for downstream analyses Differential gene expression was assessed using DESeq2 Assembly: Grcz11,Whole zebrafish larvae,Fish were exposed to retene at xxx concentrations: 0 0.205 0.512 1.28 3.2 8 20 and 50 µM,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,Zebrafish Tropical 5D line embryos were dechorionated at 4 hpf placed in 96 well plates in buffered embryo medium statically exposed to retene or vehicle control beginning at 6 hpf gently shaken overnight on an orbital shaker at 235 rpm and then sampled at xxx hpf.,timepoint:48 hpf Vehicle control|FISH strain:Tropical 5D,GSM6165378,GSM6165378: RNA Vehicle control Replicate 1; Danio rerio; RNA Seq,GSM6165378 r1,GSM6165378,1,48 hpf larvae were pooled into groups of 9 fish each briefly anesthetized on ice and excess water removed. Tissue was immediately homogenized with RNAzol RT Molecular Research Center and 0.5mm zirconium oxide beads in a Bullet Blender tissue homogenizer Next Advance. Homogenate was stored at 80 C until RNA isolation. Total RNA was isolated using a Direct zol RNA MiniPrep Kit Zymo Research with DNAse treatment. mRNA was purified using oligodT attached magnetic beads and fragmented. cDNA was synthesized using random hexamer primed reverse transcription end repaired three prime adenlylated and adapters were ligated to three prime ends. cDNA was PCR amplified.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP375841,,,Ret1_1.fq Ret1_2.fq,fastq fastq,4541215400.0,45412154.0,GSM6165378 r1,0:100 1:100,A:1200249191;C:1047425766;G:1091774738;T:1201765705;N:0,100,100,,,1200249191,1047425766,1091774738,1201765705,0,SRX15324777,SRS13053393,SRA1422455,"Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University","Robert L. Tanguay, Environmental & Molecular Toxicology, Oregon State University",1,0.9255,,0.08609,,0.70816,,0.47434,,100,,B,,usable mapping rate,bgi,bgi,3prime,poly_a,unknown,bulk,unknown,unknown,,United States,2022-05-18,Multi-stage,Multi-stage,Whole Organism,All anatomical structures 70859,SRR20789445,SRX16809298,SRS14430425,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,DTBP3,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161313N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,DTBP3,DTBP3,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,DTBP3_1.fq.gz DTBP3_2.fq.gz,fastq fastq,6640654800.0,44271032.0,DTBP3 1.fq.gz,0:150 1:150,A:1857715776;C:1468251534;G:1450498102;T:1864102458;N:86930,150,150,,,1857715776,1468251534,1450498102,1864102458,86930,SRX16809298,SRS14430425,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.87483,,0.13614,,0.69459,,0.50402,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 70860,SRR20789446,SRX16809297,SRS14430426,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,DTBP2,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161311N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,DTBP2,DTBP2,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,DTBP2_1.fq.gz DTBP2_2.fq.gz,fastq fastq,6612930300.0,44086202.0,DTBP2 1.fq.gz,0:150 1:150,A:1843555432;C:1467844074;G:1451826890;T:1849614860;N:89044,150,150,,,1843555432,1467844074,1451826890,1849614860,89044,SRX16809297,SRS14430426,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.87565,,0.13532,,0.69489,,0.49286,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 70861,SRR20789447,SRX16809296,SRS14430424,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,DTBP1,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161309N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,DTBP1,DTBP1,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,DTBP1_2.fq.gz DTBP1_1.fq.gz,fastq fastq,6661758000.0,44411720.0,DTBP1 1.fq.gz,0:150 1:150,A:1852821325;C:1483402791;G:1464548936;T:1860899167;N:85781,150,150,,,1852821325,1483402791,1464548936,1860899167,85781,SRX16809296,SRS14430424,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.85082,,0.13289,,0.69698,,0.48384,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 70862,SRR20789448,SRX16809295,SRS14430423,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,CK3,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161307N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,CK3,CK3,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,CK3_1.fq.gz CK3_2.fq.gz,fastq fastq,6632165700.0,44214438.0,CK3 1.fq.gz,0:150 1:150,A:1838766908;C:1481172882;G:1465701380;T:1846438539;N:85991,150,150,,,1838766908,1481172882,1465701380,1846438539,85991,SRX16809295,SRS14430423,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.87731,,0.13142,,0.68641,,0.48874,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 70863,SRR20789449,SRX16809294,SRS14430422,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,CK2,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161305N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,CK2,CK2,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,CK2_2.fq.gz CK2_1.fq.gz,fastq fastq,6471271800.0,43141812.0,CK2 1.fq.gz,0:150 1:150,A:2017142143;C:1222481695;G:1205635015;T:2025887170;N:125777,150,150,,,2017142143,1222481695,1205635015,2025887170,125777,SRX16809294,SRS14430422,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.82447,,0.36752,,0.80121,,0.68898,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 70864,SRR20789450,SRX16809293,SRS14430421,SRP389652,PRJNA865655,Effects of microplastic leachate and a typical plastic additive on the early development of zebrafish embryos and the gut microbiota of adult zebrafish,PRJNA865655,Other,To investigate the toxic effects of microplastic leachate and antioxidant 2 4 Di tert butylphenol 2 4 DTBP which is a composition of microplastic leachate on zebrafish embryonic development and zebrafish adult intestinal flora we collected agricultural films simulated environmental fragmentation and light processes indoors and examined microplastic leachate components. 2 4 DTBP from microplastic leachate alters the transcription levels of genes related to digestion and absorption in zebrafish larvae and the composition of intestinal flora in adult fish hinders energy uptake and utilization in zebrafish interferes with the process of glucolipid metabolism and leads to disease organ malformation and even death in zebrafish.,,,,,CK1,,strain:AB|breed:zebrafish|dev stage:96h|sex:not determined|tissue:whole organism|birth location:120.498664E、36.161303N|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of larvae from Danio rerio exposed to DMSO,CK1,CK1,tissues,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,DNBSEQ,DNBSEQ-G50,,SRP389652,,,CK1_2.fq.gz CK1_1.fq.gz,fastq fastq,6653620200.0,44357468.0,CK1 1.fq.gz,0:150 1:150,A:1846923508;C:1483544965;G:1467204186;T:1855860338;N:87203,150,150,,,1846923508,1483544965,1467204186,1855860338,87203,SRX16809293,SRS14430421,SRA1468070,Ocean University of China|College of Wnvironmental Science and Engineering,Ocean University of China,1,0.88292,,0.12768,,0.69936,,0.49774,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2022-08-03,Larval,Larval,Whole Organism,All anatomical structures 72001,SRR22193340,SRX18171781,SRS15671002,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01556,GSM6706472,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01556,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706472,GSM6706472: EOfAD like 21 01556; Danio rerio; RNA Seq,GSM6706472 r1,GSM6706472,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01556_S1_1_R2_001.fastq.gz 21-01556_S1_1_R1_001.fastq.gz,fastq fastq,3395908340.0,15435947.0,GSM6706472 r1,0:98 1:122,A:872053414;C:749104525;G:834311191;T:940344530;N:94680,98,122,,,872053414,749104525,834311191,940344530,94680,SRX18171781,SRS15671002,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92573,0.11421,0.14533,0.01898,0.66756,0.87042,0.46519,0.47753,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72002,SRR22193341,SRX18171781,SRS15671002,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01556,GSM6706472,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01556,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706472,GSM6706472: EOfAD like 21 01556; Danio rerio; RNA Seq,GSM6706472 r1,GSM6706472,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01556_S1_2_R2_001.fastq.gz 21-01556_S1_2_R1_001.fastq.gz,fastq fastq,3343026720.0,15195576.0,GSM6706472 r2,0:98 1:122,A:858208521;C:737825678;G:821458287;T:925228989;N:305245,98,122,,,858208521,737825678,821458287,925228989,305245,SRX18171781,SRS15671002,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92548,0.11575,0.14535,0.01936,0.66582,0.8661,0.46896,0.4755,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72003,SRR22193342,SRX18171781,SRS15671002,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01556,GSM6706472,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01556,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706472,GSM6706472: EOfAD like 21 01556; Danio rerio; RNA Seq,GSM6706472 r1,GSM6706472,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01556_S1_3_R2_001.fastq.gz 21-01556_S1_3_R1_001.fastq.gz,fastq fastq,3357563000.0,15261650.0,GSM6706472 r3,0:98 1:122,A:861696444;C:740875697;G:825207611;T:929559528;N:223720,98,122,,,861696444,740875697,825207611,929559528,223720,SRX18171781,SRS15671002,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92457,0.12085,0.14224,0.02009,0.66785,0.8662,0.46394,0.47687,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72004,SRR22193343,SRX18171781,SRS15671002,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01556,GSM6706472,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01556,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706472,GSM6706472: EOfAD like 21 01556; Danio rerio; RNA Seq,GSM6706472 r1,GSM6706472,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01556_S1_4_R2_001.fastq.gz 21-01556_S1_4_R1_001.fastq.gz,fastq fastq,3344014960.0,15200068.0,GSM6706472 r4,0:98 1:122,A:857807865;C:737982204;G:822436634;T:925403212;N:385045,98,122,,,857807865,737982204,822436634,925403212,385045,SRX18171781,SRS15671002,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92372,0.119,0.14466,0.0199,0.6674,0.86411,0.46687,0.4788,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72005,SRR22193344,SRX18171780,SRS15671003,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01555,GSM6706471,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01555,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706471,GSM6706471: EOfAD like 21 01555; Danio rerio; RNA Seq,GSM6706471 r1,GSM6706471,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01555_S1_1_R1_001.fastq.gz 21-01555_S1_1_R2_001.fastq.gz,fastq fastq,3708416360.0,16856438.0,GSM6706471 r1,0:98 1:122,A:935457829;C:878928090;G:898746793;T:995185121;N:98527,98,122,,,935457829,878928090,898746793,995185121,98527,SRX18171780,SRS15671003,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.9434,0.1202,0.10558,0.01322,0.66618,0.86492,0.45655,0.49167,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72006,SRR22193345,SRX18171780,SRS15671003,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01555,GSM6706471,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01555,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706471,GSM6706471: EOfAD like 21 01555; Danio rerio; RNA Seq,GSM6706471 r1,GSM6706471,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01555_S1_2_R1_001.fastq.gz 21-01555_S1_2_R2_001.fastq.gz,fastq fastq,3663468820.0,16652131.0,GSM6706471 r2,0:98 1:122,A:924148457;C:868106211;G:887682884;T:983197677;N:333591,98,122,,,924148457,868106211,887682884,983197677,333591,SRX18171780,SRS15671003,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94129,0.12102,0.10325,0.01268,0.66413,0.86413,0.45949,0.49149,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72007,SRR22193346,SRX18171780,SRS15671003,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01555,GSM6706471,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01555,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706471,GSM6706471: EOfAD like 21 01555; Danio rerio; RNA Seq,GSM6706471 r1,GSM6706471,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01555_S1_3_R1_001.fastq.gz 21-01555_S1_3_R2_001.fastq.gz,fastq fastq,3675580480.0,16707184.0,GSM6706471 r3,0:98 1:122,A:927103726;C:870783570;G:890686576;T:986764079;N:242529,98,122,,,927103726,870783570,890686576,986764079,242529,SRX18171780,SRS15671003,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94129,0.12512,0.10322,0.01341,0.66413,0.85845,0.4583,0.48736,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72008,SRR22193347,SRX18171780,SRS15671003,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01555,GSM6706471,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01555,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706471,GSM6706471: EOfAD like 21 01555; Danio rerio; RNA Seq,GSM6706471 r1,GSM6706471,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01555_S1_4_R1_001.fastq.gz 21-01555_S1_4_R2_001.fastq.gz,fastq fastq,3636975760.0,16531708.0,GSM6706471 r4,0:98 1:122,A:916721641;C:862038308;G:882219331;T:975580566;N:415914,98,122,,,916721641,862038308,882219331,975580566,415914,SRX18171780,SRS15671003,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.93964,0.12412,0.10424,0.01309,0.66659,0.86115,0.46351,0.47639,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72009,SRR22193348,SRX18171779,SRS15671001,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01554,GSM6706470,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01554,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706470,GSM6706470: wt 21 01554; Danio rerio; RNA Seq,GSM6706470 r1,GSM6706470,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01554_S1_1_R1_001.fastq.gz 21-01554_S1_1_R2_001.fastq.gz,fastq fastq,3879206760.0,17632758.0,GSM6706470 r1,0:98 1:122,A:955271885;C:904655970;G:968192563;T:1050982860;N:103482,98,122,,,955271885,904655970,968192563,1050982860,103482,SRX18171779,SRS15671001,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94363,0.11015,0.09851,0.01453,0.6663,0.87156,0.45754,0.49086,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72010,SRR22193349,SRX18171779,SRS15671001,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01554,GSM6706470,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01554,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706470,GSM6706470: wt 21 01554; Danio rerio; RNA Seq,GSM6706470 r1,GSM6706470,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01554_S1_2_R1_001.fastq.gz 21-01554_S1_2_R2_001.fastq.gz,fastq fastq,3824753240.0,17385242.0,GSM6706470 r2,0:98 1:122,A:941784598;C:892008207;G:954347307;T:1036263967;N:349161,98,122,,,941784598,892008207,954347307,1036263967,349161,SRX18171779,SRS15671001,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94106,0.1102,0.09774,0.01421,0.66756,0.87089,0.45471,0.4985,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72011,SRR22193350,SRX18171779,SRS15671001,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01554,GSM6706470,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01554,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706470,GSM6706470: wt 21 01554; Danio rerio; RNA Seq,GSM6706470 r1,GSM6706470,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01554_S1_3_R1_001.fastq.gz 21-01554_S1_3_R2_001.fastq.gz,fastq fastq,3835151100.0,17432505.0,GSM6706470 r3,0:98 1:122,A:944134506;C:894212763;G:957158243;T:1039392488;N:253100,98,122,,,944134506,894212763,957158243,1039392488,253100,SRX18171779,SRS15671001,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94266,0.11382,0.09715,0.01435,0.66858,0.86912,0.45834,0.48812,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72012,SRR22193351,SRX18171779,SRS15671001,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01554,GSM6706470,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01554,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706470,GSM6706470: wt 21 01554; Danio rerio; RNA Seq,GSM6706470 r1,GSM6706470,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01554_S1_4_R1_001.fastq.gz 21-01554_S1_4_R2_001.fastq.gz,fastq fastq,3802192460.0,17282693.0,GSM6706470 r4,0:98 1:122,A:935684594;C:886400099;G:949729093;T:1029943566;N:435108,98,122,,,935684594,886400099,949729093,1029943566,435108,SRX18171779,SRS15671001,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94073,0.11283,0.09612,0.01398,0.66612,0.86827,0.45857,0.4967,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72013,SRR22193352,SRX18171778,SRS15671000,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01553,GSM6706469,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01553,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706469,GSM6706469: wt 21 01553; Danio rerio; RNA Seq,GSM6706469 r1,GSM6706469,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01553_S1_1_R2_001.fastq.gz 21-01553_S1_1_R1_001.fastq.gz,fastq fastq,3825210620.0,17387321.0,GSM6706469 r1,0:98 1:122,A:940873078;C:927434118;G:921037289;T:1035762155;N:103980,98,122,,,940873078,927434118,921037289,1035762155,103980,SRX18171778,SRS15671000,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94322,0.11052,0.09983,0.01143,0.66569,0.86951,0.46556,0.46262,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72014,SRR22193353,SRX18171778,SRS15671000,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01553,GSM6706469,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01553,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706469,GSM6706469: wt 21 01553; Danio rerio; RNA Seq,GSM6706469 r1,GSM6706469,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01553_S1_2_R2_001.fastq.gz 21-01553_S1_2_R1_001.fastq.gz,fastq fastq,3770888880.0,17140404.0,GSM6706469 r2,0:98 1:122,A:927579411;C:914235370;G:907389452;T:1021339869;N:344778,98,122,,,927579411,914235370,907389452,1021339869,344778,SRX18171778,SRS15671000,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94089,0.11322,0.10027,0.01194,0.66496,0.86632,0.45313,0.45403,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72015,SRR22193354,SRX18171778,SRS15671000,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01553,GSM6706469,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01553,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706469,GSM6706469: wt 21 01553; Danio rerio; RNA Seq,GSM6706469 r1,GSM6706469,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01553_S1_3_R2_001.fastq.gz 21-01553_S1_3_R1_001.fastq.gz,fastq fastq,3763934680.0,17108794.0,GSM6706469 r3,0:98 1:122,A:925863278;C:912340582;G:905682568;T:1019798572;N:249680,98,122,,,925863278,912340582,905682568,1019798572,249680,SRX18171778,SRS15671000,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94158,0.11605,0.10081,0.0121,0.66626,0.86427,0.45341,0.46509,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72016,SRR22193355,SRX18171778,SRS15671000,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01553,GSM6706469,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01553,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706469,GSM6706469: wt 21 01553; Danio rerio; RNA Seq,GSM6706469 r1,GSM6706469,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01553_S1_4_R2_001.fastq.gz 21-01553_S1_4_R1_001.fastq.gz,fastq fastq,3737736200.0,16989710.0,GSM6706469 r4,0:98 1:122,A:918895394;C:906324681;G:900093790;T:1011994954;N:427381,98,122,,,918895394,906324681,900093790,1011994954,427381,SRX18171778,SRS15671000,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94033,0.11426,0.09974,0.01196,0.6644,0.86726,0.46134,0.48323,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72017,SRR22193356,SRX18171777,SRS15670999,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01552,GSM6706468,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01552,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706468,GSM6706468: wt 21 01552; Danio rerio; RNA Seq,GSM6706468 r1,GSM6706468,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01552_S1_1_R2_001.fastq.gz 21-01552_S1_1_R1_001.fastq.gz,fastq fastq,3712516500.0,16875075.0,GSM6706468 r1,0:98 1:122,A:927402288;C:847915700;G:909785870;T:1027312056;N:100586,98,122,,,927402288,847915700,909785870,1027312056,100586,SRX18171777,SRS15670999,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.93024,0.09552,0.13652,0.01058,0.66423,0.88276,0.46693,0.48685,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72018,SRR22193357,SRX18171777,SRS15670999,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01552,GSM6706468,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01552,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706468,GSM6706468: wt 21 01552; Danio rerio; RNA Seq,GSM6706468 r1,GSM6706468,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01552_S1_2_R2_001.fastq.gz 21-01552_S1_2_R1_001.fastq.gz,fastq fastq,3662336700.0,16646985.0,GSM6706468 r2,0:98 1:122,A:914811564;C:836467540;G:897331475;T:1013391863;N:334258,98,122,,,914811564,836467540,897331475,1013391863,334258,SRX18171777,SRS15670999,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92904,0.09798,0.13484,0.01043,0.66513,0.88114,0.46739,0.49463,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72019,SRR22193358,SRX18171777,SRS15670999,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01552,GSM6706468,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01552,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706468,GSM6706468: wt 21 01552; Danio rerio; RNA Seq,GSM6706468 r1,GSM6706468,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01552_S1_3_R2_001.fastq.gz 21-01552_S1_3_R1_001.fastq.gz,fastq fastq,3669312020.0,16678691.0,GSM6706468 r3,0:98 1:122,A:916361469;C:837961584;G:899113084;T:1015632911;N:242972,98,122,,,916361469,837961584,899113084,1015632911,242972,SRX18171777,SRS15670999,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92932,0.10276,0.13406,0.01137,0.6631,0.87866,0.46032,0.48774,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72020,SRR22193359,SRX18171777,SRS15670999,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01552,GSM6706468,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01552,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706468,GSM6706468: wt 21 01552; Danio rerio; RNA Seq,GSM6706468 r1,GSM6706468,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01552_S1_4_R1_001.fastq.gz 21-01552_S1_4_R2_001.fastq.gz,fastq fastq,3636707800.0,16530490.0,GSM6706468 r4,0:98 1:122,A:907592886;C:830893111;G:891977210;T:1005830743;N:413850,98,122,,,907592886,830893111,891977210,1005830743,413850,SRX18171777,SRS15670999,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92762,0.10027,0.13527,0.01083,0.66578,0.88045,0.46575,0.49088,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72021,SRR22193360,SRX18171776,SRS15670998,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01551,GSM6706467,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01551,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706467,GSM6706467: MPS IIIB 21 01551; Danio rerio; RNA Seq,GSM6706467 r1,GSM6706467,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01551_S1_1_R1_001.fastq.gz 21-01551_S1_1_R2_001.fastq.gz,fastq fastq,3840710500.0,17457775.0,GSM6706467 r1,0:98 1:122,A:953722428;C:945847269;G:896745422;T:1044291298;N:104083,98,122,,,953722428,945847269,896745422,1044291298,104083,SRX18171776,SRS15670998,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94489,0.11229,0.10592,0.01512,0.6622,0.86766,0.46952,0.49661,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72022,SRR22193361,SRX18171776,SRS15670998,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01551,GSM6706467,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01551,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706467,GSM6706467: MPS IIIB 21 01551; Danio rerio; RNA Seq,GSM6706467 r1,GSM6706467,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01551_S1_2_R2_001.fastq.gz 21-01551_S1_2_R1_001.fastq.gz,fastq fastq,3799023580.0,17268289.0,GSM6706467 r2,0:98 1:122,A:943528032;C:935393046;G:886508478;T:1033245874;N:348150,98,122,,,943528032,935393046,886508478,1033245874,348150,SRX18171776,SRS15670998,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94185,0.11582,0.1051,0.01508,0.66239,0.8645,0.45977,0.50377,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72023,SRR22193362,SRX18171776,SRS15670998,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01551,GSM6706467,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01551,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706467,GSM6706467: MPS IIIB 21 01551; Danio rerio; RNA Seq,GSM6706467 r1,GSM6706467,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01551_S1_3_R1_001.fastq.gz 21-01551_S1_3_R2_001.fastq.gz,fastq fastq,3808384580.0,17310839.0,GSM6706467 r3,0:98 1:122,A:945747939;C:937533782;G:888747219;T:1036104761;N:250879,98,122,,,945747939,937533782,888747219,1036104761,250879,SRX18171776,SRS15670998,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94279,0.11904,0.10554,0.01608,0.66395,0.86206,0.47001,0.49561,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72024,SRR22193363,SRX18171776,SRS15670998,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01551,GSM6706467,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01551,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706467,GSM6706467: MPS IIIB 21 01551; Danio rerio; RNA Seq,GSM6706467 r1,GSM6706467,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01551_S1_4_R2_001.fastq.gz 21-01551_S1_4_R1_001.fastq.gz,fastq fastq,3772018140.0,17145537.0,GSM6706467 r4,0:98 1:122,A:936143571;C:928832484;G:881223581;T:1025385479;N:433025,98,122,,,936143571,928832484,881223581,1025385479,433025,SRX18171776,SRS15670998,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94179,0.11909,0.10556,0.01559,0.66369,0.86133,0.47163,0.49444,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72025,SRR22193364,SRX18171775,SRS15670997,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01549,GSM6706466,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01549,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706466,GSM6706466: MPS IIIB 21 01549; Danio rerio; RNA Seq,GSM6706466 r1,GSM6706466,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01549_S1_1_R1_001.fastq.gz 21-01549_S1_1_R2_001.fastq.gz,fastq fastq,4012933320.0,18240606.0,GSM6706466 r1,0:98 1:122,A:968481998;C:920364942;G:1020973420;T:1103007407;N:105553,98,122,,,968481998,920364942,1020973420,1103007407,105553,SRX18171775,SRS15670997,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94728,0.10187,0.09688,0.00845,0.66616,0.88099,0.47287,0.49136,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72026,SRR22193365,SRX18171775,SRS15670997,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01549,GSM6706466,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01549,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706466,GSM6706466: MPS IIIB 21 01549; Danio rerio; RNA Seq,GSM6706466 r1,GSM6706466,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01549_S1_2_R1_001.fastq.gz 21-01549_S1_2_R2_001.fastq.gz,fastq fastq,3966032180.0,18027419.0,GSM6706466 r2,0:98 1:122,A:957215620;C:909378774;G:1008595074;T:1090481705;N:361007,98,122,,,957215620,909378774,1008595074,1090481705,361007,SRX18171775,SRS15670997,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94506,0.10427,0.09622,0.00852,0.66707,0.8771,0.47144,0.48709,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72027,SRR22193366,SRX18171775,SRS15670997,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01549,GSM6706466,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01549,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706466,GSM6706466: MPS IIIB 21 01549; Danio rerio; RNA Seq,GSM6706466 r1,GSM6706466,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01549_S1_3_R1_001.fastq.gz 21-01549_S1_3_R2_001.fastq.gz,fastq fastq,3979290040.0,18087682.0,GSM6706466 r3,0:98 1:122,A:960373281;C:912191453;G:1011910478;T:1094554245;N:260583,98,122,,,960373281,912191453,1011910478,1094554245,260583,SRX18171775,SRS15670997,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94591,0.10691,0.09506,0.00832,0.66815,0.87547,0.46675,0.49141,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72028,SRR22193367,SRX18171775,SRS15670997,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01549,GSM6706466,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01549,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706466,GSM6706466: MPS IIIB 21 01549; Danio rerio; RNA Seq,GSM6706466 r1,GSM6706466,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01549_S1_4_R1_001.fastq.gz 21-01549_S1_4_R2_001.fastq.gz,fastq fastq,3950836340.0,17958347.0,GSM6706466 r4,0:98 1:122,A:952986092;C:906017140;G:1005513937;T:1085871362;N:447809,98,122,,,952986092,906017140,1005513937,1085871362,447809,SRX18171775,SRS15670997,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94349,0.1071,0.09625,0.00814,0.66691,0.87428,0.47077,0.50094,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72029,SRR22193368,SRX18171774,SRS15670996,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01548,GSM6706465,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01548,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706465,GSM6706465: MPS IIIB 21 01548; Danio rerio; RNA Seq,GSM6706465 r1,GSM6706465,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01548_S1_1_R1_001.fastq.gz 21-01548_S1_1_R2_001.fastq.gz,fastq fastq,3335864400.0,15163020.0,GSM6706465 r1,0:98 1:122,A:849250493;C:698687909;G:846014224;T:941822144;N:89630,98,122,,,849250493,698687909,846014224,941822144,89630,SRX18171774,SRS15670996,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92049,0.0976,0.16956,0.01366,0.66663,0.88345,0.4626,0.48535,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72030,SRR22193369,SRX18171774,SRS15670996,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01548,GSM6706465,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01548,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706465,GSM6706465: MPS IIIB 21 01548; Danio rerio; RNA Seq,GSM6706465 r1,GSM6706465,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01548_S1_2_R1_001.fastq.gz 21-01548_S1_2_R2_001.fastq.gz,fastq fastq,3300739860.0,15003363.0,GSM6706465 r2,0:98 1:122,A:840289029;C:691317210;G:836811179;T:932021734;N:300708,98,122,,,840289029,691317210,836811179,932021734,300708,SRX18171774,SRS15670996,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.91831,0.1014,0.16629,0.01407,0.66782,0.87795,0.46148,0.49464,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72031,SRR22193370,SRX18171774,SRS15670996,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01548,GSM6706465,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01548,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706465,GSM6706465: MPS IIIB 21 01548; Danio rerio; RNA Seq,GSM6706465 r1,GSM6706465,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01548_S1_3_R1_001.fastq.gz 21-01548_S1_3_R2_001.fastq.gz,fastq fastq,3306512220.0,15029601.0,GSM6706465 r3,0:98 1:122,A:841442672;C:692536122;G:838407700;T:933906481;N:219245,98,122,,,841442672,692536122,838407700,933906481,219245,SRX18171774,SRS15670996,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92016,0.10472,0.1666,0.01432,0.66766,0.87702,0.46197,0.47934,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72032,SRR22193371,SRX18171774,SRS15670996,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01548,GSM6706465,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01548,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706465,GSM6706465: MPS IIIB 21 01548; Danio rerio; RNA Seq,GSM6706465 r1,GSM6706465,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01548_S1_4_R1_001.fastq.gz 21-01548_S1_4_R2_001.fastq.gz,fastq fastq,3279224520.0,14905566.0,GSM6706465 r4,0:98 1:122,A:834099389;C:686963420;G:832147685;T:925643934;N:370092,98,122,,,834099389,686963420,832147685,925643934,370092,SRX18171774,SRS15670996,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.91687,0.10365,0.16489,0.01376,0.66716,0.8747,0.46317,0.48485,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72033,SRR22193372,SRX18171773,SRS15670995,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01545,GSM6706464,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01545,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706464,GSM6706464: wt 21 01545; Danio rerio; RNA Seq,GSM6706464 r1,GSM6706464,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01545_S1_1_R1_001.fastq.gz 21-01545_S1_1_R2_001.fastq.gz,fastq fastq,3537288040.0,16078582.0,GSM6706464 r1,0:98 1:122,A:919278297;C:840633603;G:866375931;T:910902834;N:97375,98,122,,,919278297,840633603,866375931,910902834,97375,SRX18171773,SRS15670995,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94245,0.10444,0.09824,0.00843,0.66515,0.876,0.46549,0.48641,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72034,SRR22193373,SRX18171773,SRS15670995,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01545,GSM6706464,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01545,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706464,GSM6706464: wt 21 01545; Danio rerio; RNA Seq,GSM6706464 r1,GSM6706464,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01545_S1_2_R1_001.fastq.gz 21-01545_S1_2_R2_001.fastq.gz,fastq fastq,3482959700.0,15831635.0,GSM6706464 r2,0:98 1:122,A:905038217;C:827663889;G:852963269;T:896972365;N:321960,98,122,,,905038217,827663889,852963269,896972365,321960,SRX18171773,SRS15670995,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.93932,0.10652,0.09583,0.00877,0.66689,0.87409,0.46557,0.48057,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72035,SRR22193374,SRX18171773,SRS15670995,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01545,GSM6706464,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01545,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706464,GSM6706464: wt 21 01545; Danio rerio; RNA Seq,GSM6706464 r1,GSM6706464,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01545_S1_3_R1_001.fastq.gz 21-01545_S1_3_R2_001.fastq.gz,fastq fastq,3495495520.0,15888616.0,GSM6706464 r3,0:98 1:122,A:908195450;C:830469880;G:856006468;T:900592133;N:231589,98,122,,,908195450,830469880,856006468,900592133,231589,SRX18171773,SRS15670995,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94106,0.11014,0.09789,0.00915,0.66289,0.87095,0.45982,0.47599,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72036,SRR22193375,SRX18171773,SRS15670995,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01545,GSM6706464,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01545,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706464,GSM6706464: wt 21 01545; Danio rerio; RNA Seq,GSM6706464 r1,GSM6706464,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01545_S1_4_R1_001.fastq.gz 21-01545_S1_4_R2_001.fastq.gz,fastq fastq,3442751180.0,15648869.0,GSM6706464 r4,0:98 1:122,A:893810866;C:818316932;G:844064771;T:886162350;N:396261,98,122,,,893810866,818316932,844064771,886162350,396261,SRX18171773,SRS15670995,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94013,0.11023,0.09707,0.00898,0.66407,0.86977,0.46443,0.48099,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72037,SRR22193376,SRX18171772,SRS15670994,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01544,GSM6706463,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01544,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706463,GSM6706463: MPS IIIB 21 01544; Danio rerio; RNA Seq,GSM6706463 r1,GSM6706463,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01544_S1_1_R1_001.fastq.gz 21-01544_S1_1_R2_001.fastq.gz,fastq fastq,3569650920.0,16225686.0,GSM6706463 r1,0:98 1:122,A:929975667;C:815491785;G:870925137;T:953159293;N:99038,98,122,,,929975667,815491785,870925137,953159293,99038,SRX18171772,SRS15670994,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.93153,0.1135,0.13245,0.01254,0.6616,0.86787,0.46243,0.4871,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72038,SRR22193377,SRX18171772,SRS15670994,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01544,GSM6706463,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01544,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706463,GSM6706463: MPS IIIB 21 01544; Danio rerio; RNA Seq,GSM6706463 r1,GSM6706463,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01544_S1_2_R1_001.fastq.gz 21-01544_S1_2_R2_001.fastq.gz,fastq fastq,3516174640.0,15982612.0,GSM6706463 r2,0:98 1:122,A:915863681;C:803433150;G:857804994;T:938749546;N:323269,98,122,,,915863681,803433150,857804994,938749546,323269,SRX18171772,SRS15670994,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92961,0.11481,0.12979,0.01314,0.66038,0.86744,0.4601,0.49316,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72039,SRR22193378,SRX18171772,SRS15670994,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01544,GSM6706463,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01544,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706463,GSM6706463: MPS IIIB 21 01544; Danio rerio; RNA Seq,GSM6706463 r1,GSM6706463,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01544_S1_3_R1_001.fastq.gz 21-01544_S1_3_R2_001.fastq.gz,fastq fastq,3523057120.0,16013896.0,GSM6706463 r3,0:98 1:122,A:917508344;C:804911842;G:859592449;T:940811168;N:233317,98,122,,,917508344,804911842,859592449,940811168,233317,SRX18171772,SRS15670994,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.93,0.11944,0.13017,0.01315,0.66133,0.8631,0.46256,0.49748,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72040,SRR22193379,SRX18171772,SRS15670994,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,MPS IIIB 21 01544,GSM6706463,,source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,MPS IIIB 21 01544,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf,GSM6706463,GSM6706463: MPS IIIB 21 01544; Danio rerio; RNA Seq,GSM6706463 r1,GSM6706463,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01544_S1_4_R1_001.fastq.gz 21-01544_S1_4_R2_001.fastq.gz,fastq fastq,3468610420.0,15766411.0,GSM6706463 r4,0:98 1:122,A:902532448;C:792788028;G:847364948;T:925526873;N:398123,98,122,,,902532448,792788028,847364948,925526873,398123,SRX18171772,SRS15670994,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.92929,0.11832,0.13134,0.01296,0.66141,0.8636,0.46452,0.49638,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72041,SRR22193380,SRX18171771,SRS15670993,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01543,GSM6706462,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01543,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706462,GSM6706462: wt 21 01543; Danio rerio; RNA Seq,GSM6706462 r1,GSM6706462,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01543_S1_1_R1_001.fastq.gz 21-01543_S1_1_R2_001.fastq.gz,fastq fastq,3962241360.0,18010188.0,GSM6706462 r1,0:98 1:122,A:1005899931;C:967194519;G:960640294;T:1028402649;N:103967,98,122,,,1005899931,967194519,960640294,1028402649,103967,SRX18171771,SRS15670993,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.9468,0.10218,0.09587,0.00837,0.67176,0.87905,0.45938,0.49304,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72042,SRR22193381,SRX18171771,SRS15670993,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01543,GSM6706462,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01543,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706462,GSM6706462: wt 21 01543; Danio rerio; RNA Seq,GSM6706462 r1,GSM6706462,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01543_S1_2_R2_001.fastq.gz 21-01543_S1_2_R1_001.fastq.gz,fastq fastq,3911739480.0,17780634.0,GSM6706462 r2,0:98 1:122,A:993189409;C:954682736;G:947951757;T:1015554961;N:360617,98,122,,,993189409,954682736,947951757,1015554961,360617,SRX18171771,SRS15670993,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94526,0.10376,0.0951,0.00879,0.67405,0.87834,0.46395,0.5063,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72043,SRR22193382,SRX18171771,SRS15670993,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01543,GSM6706462,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01543,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706462,GSM6706462: wt 21 01543; Danio rerio; RNA Seq,GSM6706462 r1,GSM6706462,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01543_S1_3_R1_001.fastq.gz 21-01543_S1_3_R2_001.fastq.gz,fastq fastq,3938324500.0,17901475.0,GSM6706462 r3,0:98 1:122,A:999770376;C:960889809;G:954549762;T:1022852193;N:262360,98,122,,,999770376,960889809,954549762,1022852193,262360,SRX18171771,SRS15670993,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94485,0.10665,0.09506,0.00864,0.67269,0.87578,0.46731,0.50148,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72044,SRR22193383,SRX18171771,SRS15670993,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,wt 21 01543,GSM6706462,,source name:whole larvae|tissue:whole larvae|genotype:WT|developmental stage:7 dpf,wt 21 01543,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:WT|developmental stage:7 dpf,GSM6706462,GSM6706462: wt 21 01543; Danio rerio; RNA Seq,GSM6706462 r1,GSM6706462,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01543_S1_4_R1_001.fastq.gz 21-01543_S1_4_R2_001.fastq.gz,fastq fastq,3862683000.0,17557650.0,GSM6706462 r4,0:98 1:122,A:979875117;C:943011430;G:937135707;T:1002216102;N:444644,98,122,,,979875117,943011430,937135707,1002216102,444644,SRX18171771,SRS15670993,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.94418,0.10622,0.09399,0.00861,0.67235,0.8733,0.46777,0.49519,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72045,SRR22193384,SRX18171770,SRS15670992,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01542,GSM6706461,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01542,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706461,GSM6706461: EOfAD like 21 01542; Danio rerio; RNA Seq,GSM6706461 r1,GSM6706461,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01542_S1_1_R2_001.fastq.gz 21-01542_S1_1_R1_001.fastq.gz,fastq fastq,3786915660.0,17213253.0,GSM6706461 r1,0:98 1:122,A:931135195;C:913231625;G:912750141;T:1029697506;N:101193,98,122,,,931135195,913231625,912750141,1029697506,101193,SRX18171770,SRS15670992,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.90426,0.09579,0.09759,0.00909,0.67767,0.88436,0.46287,0.48637,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures 72046,SRR22193385,SRX18171770,SRS15670992,SRP406332,PRJNA898346,Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae,GSE217196,Transcriptome Analysis,Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III MPSIII is an extreme consequence of ELP dysfunction where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide which ultimately accumulates and interferes with the function of the ELP. Unlike AD Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes they likely share disease associated mechanisms. Here we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 µL of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4°C. Then the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.,,pubmed:36945478;pubmed:38346074,,EOfAD like 21 01542,GSM6706461,,source name:whole larvae|tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,EOfAD like 21 01542,98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts,whole larvae,whole larvae were treated with RNAlater solution to stabilise RNA.,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,The larvae were raised in E3 medium for 7 days allowing complete larval yolk absorption but not food intake,tissue:whole larvae|genotype:EOfAD like|developmental stage:7 dpf,GSM6706461,GSM6706461: EOfAD like 21 01542; Danio rerio; RNA Seq,GSM6706461 r1,GSM6706461,1,Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion Life Technologies Thermo Fisher Scientific Waltham MA USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508 protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-G400,,SRP406332,,loader:fastq load.py,21-01542_S1_2_R2_001.fastq.gz 21-01542_S1_2_R1_001.fastq.gz,fastq fastq,3740695420.0,17003161.0,GSM6706461 r2,0:98 1:122,A:919823770;C:901874910;G:901383110;T:1017269925;N:343705,98,122,,,919823770,901874910,901383110,1017269925,343705,SRX18171770,SRS15670992,SRA1534778,The University of Adelaide,The University of Adelaide,2,0.90187,0.09867,0.09882,0.00956,0.68065,0.8856,0.46403,0.48795,98,122,B,T,mate2 technical by mapping diff,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2022-11-03,Larval,Larval,Whole Organism,All anatomical structures