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196 rows where experiment.platform = "DNBSEQ", technology = "unknown" and tissue_curation = "Whole Organism"

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devstage_curation 5

devstage_curation_coarse 3

experiment.library_selection 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 196 ✖

technology 1

  • unknown · 196 ✖

experiment.platform 1

  • DNBSEQ · 196 ✖

experiment.library_strategy 1

experiment.library_source 1

experiment.library_layout 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
68685 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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 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…   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

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