{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.platform = \"DNBSEQ\", technology = \"unknown\" and tissue_curation = \"Brain\"", "rows": [[26386, "SRR25917801", "SRX21637674", "SRS18807763", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. 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We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. 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We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02952", "GSM7761846", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.8|geo loc name:missing|collection date:missing", "22 02952", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.8", "GSM7761846", "GSM7761846: 22 02952; Danio rerio; RNA Seq", "GSM7761846 r1", "GSM7761846", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02952_S23_L04_R1_001.fastq.gz 22-02952_S23_L04_R2_001.fastq.gz", "fastq fastq", 3963250536.0, 20220666.0, "GSM7761846 r4", "0:98 1:98", "A:1045663273;C:926206212;G:924140110;T:1067139742;N:101199", 98, 98, null, null, 1045663273, 926206212, 924140110, 1067139742, 101199, "SRX21637673", "SRS18807762", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94449, 0.94083, 0.10086, 0.10197, 0.70469, 0.70569, 0.4991, 0.49202, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26394, "SRR25917809", "SRX21637672", "SRS18807761", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02951", "GSM7761845", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing", "22 02951", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7", "GSM7761845", "GSM7761845: 22 02951; Danio rerio; RNA Seq", "GSM7761845 r1", "GSM7761845", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02951_S22_L01_R1_001.fastq.gz 22-02951_S22_L01_R2_001.fastq.gz", "fastq fastq", 2029687408.0, 10355548.0, "GSM7761845 r1", "0:98 1:98", "A:538688097;C:471579919;G:470623522;T:547765689;N:1030181", 98, 98, null, null, 538688097, 471579919, 470623522, 547765689, 1030181, "SRX21637672", "SRS18807761", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.92721, 0.92969, 0.09472, 0.09676, 0.70423, 0.70276, 0.49981, 0.49898, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26395, "SRR25917810", "SRX21637672", "SRS18807761", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02951", "GSM7761845", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing", "22 02951", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7", "GSM7761845", "GSM7761845: 22 02951; Danio rerio; RNA Seq", "GSM7761845 r1", "GSM7761845", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02951_S22_L02_R1_001.fastq.gz 22-02951_S22_L02_R2_001.fastq.gz", "fastq fastq", 3072360760.0, 15675310.0, "GSM7761845 r2", "0:98 1:98", "A:810685642;C:719109817;G:718137072;T:824036555;N:391674", 98, 98, null, null, 810685642, 719109817, 718137072, 824036555, 391674, "SRX21637672", "SRS18807761", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9358, 0.93813, 0.09385, 0.09614, 0.70341, 0.70303, 0.49098, 0.49194, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26396, "SRR25917811", "SRX21637672", "SRS18807761", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02951", "GSM7761845", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing", "22 02951", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7", "GSM7761845", "GSM7761845: 22 02951; Danio rerio; RNA Seq", "GSM7761845 r1", "GSM7761845", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02951_S22_L03_R1_001.fastq.gz 22-02951_S22_L03_R2_001.fastq.gz", "fastq fastq", 2765019432.0, 14107242.0, "GSM7761845 r3", "0:98 1:98", "A:730929526;C:644675885;G:644121852;T:744649936;N:642233", 98, 98, null, null, 730929526, 644675885, 644121852, 744649936, 642233, "SRX21637672", "SRS18807761", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93375, 0.93756, 0.0926, 0.09517, 0.70429, 0.70358, 0.50064, 0.50166, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26397, "SRR25917812", "SRX21637672", "SRS18807761", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02951", "GSM7761845", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.7|geo loc name:missing|collection date:missing", "22 02951", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.7", "GSM7761845", "GSM7761845: 22 02951; Danio rerio; RNA Seq", "GSM7761845 r1", "GSM7761845", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02951_S22_L04_R1_001.fastq.gz 22-02951_S22_L04_R2_001.fastq.gz", "fastq fastq", 4491524436.0, 22915941.0, "GSM7761845 r4", "0:98 1:98", "A:1183373286;C:1051469132;G:1052482979;T:1204083766;N:115273", 98, 98, null, null, 1183373286, 1051469132, 1052482979, 1204083766, 115273, "SRX21637672", "SRS18807761", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94091, 0.94403, 0.09318, 0.09521, 0.70374, 0.70234, 0.49577, 0.49187, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26398, "SRR25917813", "SRX21637671", "SRS18807760", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02949", "GSM7761844", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing", "22 02949", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7", "GSM7761844", "GSM7761844: 22 02949; Danio rerio; RNA Seq", "GSM7761844 r1", "GSM7761844", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02949_S21_L01_R1_001.fastq.gz 22-02949_S21_L01_R2_001.fastq.gz", "fastq fastq", 2534565376.0, 12931456.0, "GSM7761844 r1", "0:98 1:98", "A:674884849;C:586725099;G:584045434;T:687552587;N:1357407", 98, 98, null, null, 674884849, 586725099, 584045434, 687552587, 1357407, "SRX21637671", "SRS18807760", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93278, 0.9279, 0.10047, 0.10166, 0.70506, 0.70461, 0.51365, 0.5138, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26399, "SRR25917814", "SRX21637671", "SRS18807760", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02949", "GSM7761844", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing", "22 02949", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7", "GSM7761844", "GSM7761844: 22 02949; Danio rerio; RNA Seq", "GSM7761844 r1", "GSM7761844", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02949_S21_L02_R1_001.fastq.gz 22-02949_S21_L02_R2_001.fastq.gz", "fastq fastq", 3889732308.0, 19845573.0, "GSM7761844 r2", "0:98 1:98", "A:1029905526;C:906662466;G:903535838;T:1049088768;N:539710", 98, 98, null, null, 1029905526, 906662466, 903535838, 1049088768, 539710, "SRX21637671", "SRS18807760", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94166, 0.93609, 0.09893, 0.10006, 0.70313, 0.70439, 0.51404, 0.50855, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26400, "SRR25917815", "SRX21637671", "SRS18807760", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02949", "GSM7761844", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing", "22 02949", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7", "GSM7761844", "GSM7761844: 22 02949; Danio rerio; RNA Seq", "GSM7761844 r1", "GSM7761844", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02949_S21_L03_R1_001.fastq.gz 22-02949_S21_L03_R2_001.fastq.gz", "fastq fastq", 3291066380.0, 16791155.0, "GSM7761844 r3", "0:98 1:98", "A:872393079;C:764845510;G:762405303;T:890638586;N:783902", 98, 98, null, null, 872393079, 764845510, 762405303, 890638586, 783902, "SRX21637671", "SRS18807760", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94062, 0.93691, 0.09836, 0.0996, 0.70416, 0.70461, 0.51782, 0.50965, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26401, "SRR25917816", "SRX21637671", "SRS18807760", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02949", "GSM7761844", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:3|rin:9.7|geo loc name:missing|collection date:missing", "22 02949", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:3|rin:9.7", "GSM7761844", "GSM7761844: 22 02949; Danio rerio; RNA Seq", "GSM7761844 r1", "GSM7761844", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02949_S21_L04_R1_001.fastq.gz 22-02949_S21_L04_R2_001.fastq.gz", "fastq fastq", 5366313988.0, 27379153.0, "GSM7761844 r4", "0:98 1:98", "A:1415961559;C:1253439804;G:1252742067;T:1444033449;N:137109", 98, 98, null, null, 1415961559, 1253439804, 1252742067, 1444033449, 137109, "SRX21637671", "SRS18807760", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94568, 0.94293, 0.09906, 0.10054, 0.70402, 0.7052, 0.51461, 0.52073, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26402, "SRR25917817", "SRX21637670", "SRS18807759", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02948", "GSM7761843", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02948", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761843", "GSM7761843: 22 02948; Danio rerio; RNA Seq", "GSM7761843 r1", "GSM7761843", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02948_S20_L01_R1_001.fastq.gz 22-02948_S20_L01_R2_001.fastq.gz", "fastq fastq", 2053905168.0, 10479108.0, "GSM7761843 r1", "0:98 1:98", "A:547671134;C:475089537;G:473080534;T:556992811;N:1071152", 98, 98, null, null, 547671134, 475089537, 473080534, 556992811, 1071152, "SRX21637670", "SRS18807759", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93522, 0.9298, 0.10197, 0.10238, 0.70339, 0.70421, 0.50454, 0.50393, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26403, "SRR25917818", "SRX21637670", "SRS18807759", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02948", "GSM7761843", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02948", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761843", "GSM7761843: 22 02948; Danio rerio; RNA Seq", "GSM7761843 r1", "GSM7761843", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02948_S20_L02_R1_001.fastq.gz 22-02948_S20_L02_R2_001.fastq.gz", "fastq fastq", 3144952300.0, 16045675.0, "GSM7761843 r2", "0:98 1:98", "A:832655138;C:733701092;G:731348360;T:846811030;N:436680", 98, 98, null, null, 832655138, 733701092, 731348360, 846811030, 436680, "SRX21637670", "SRS18807759", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94365, 0.93984, 0.10028, 0.10124, 0.70398, 0.70565, 0.50353, 0.50505, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26404, "SRR25917819", "SRX21637670", "SRS18807759", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02948", "GSM7761843", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02948", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761843", "GSM7761843: 22 02948; Danio rerio; RNA Seq", "GSM7761843 r1", "GSM7761843", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02948_S20_L03_R1_001.fastq.gz 22-02948_S20_L03_R2_001.fastq.gz", "fastq fastq", 2460170244.0, 12551889.0, "GSM7761843 r3", "0:98 1:98", "A:651706233;C:572474025;G:570982999;T:664399947;N:607040", 98, 98, null, null, 651706233, 572474025, 570982999, 664399947, 607040, "SRX21637670", "SRS18807759", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9411, 0.93886, 0.09891, 0.10006, 0.70485, 0.70362, 0.50337, 0.50208, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26405, "SRR25917820", "SRX21637670", "SRS18807759", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02948", "GSM7761843", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02948", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761843", "GSM7761843: 22 02948; Danio rerio; RNA Seq", "GSM7761843 r1", "GSM7761843", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02948_S20_L04_R1_001.fastq.gz 22-02948_S20_L04_R2_001.fastq.gz", "fastq fastq", 3890916344.0, 19851614.0, "GSM7761843 r4", "0:98 1:98", "A:1025556861;C:910441322;G:909593603;T:1045230061;N:94497", 98, 98, null, null, 1025556861, 910441322, 909593603, 1045230061, 94497, "SRX21637670", "SRS18807759", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94835, 0.94517, 0.09781, 0.09849, 0.70274, 0.70374, 0.5027, 0.5008, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26406, "SRR25917821", "SRX21637669", "SRS18807758", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02947", "GSM7761842", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing", "22 02947", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6", "GSM7761842", "GSM7761842: 22 02947; Danio rerio; RNA Seq", "GSM7761842 r1", "GSM7761842", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02947_S19_L01_R1_001.fastq.gz 22-02947_S19_L01_R2_001.fastq.gz", "fastq fastq", 1696563848.0, 8655938.0, "GSM7761842 r1", "0:98 1:98", "A:453186259;C:391677304;G:390304899;T:460508753;N:886633", 98, 98, null, null, 453186259, 391677304, 390304899, 460508753, 886633, "SRX21637669", "SRS18807758", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9329, 0.92803, 0.10284, 0.10415, 0.70611, 0.70664, 0.49615, 0.49305, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26407, "SRR25917822", "SRX21637669", "SRS18807758", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02947", "GSM7761842", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing", "22 02947", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6", "GSM7761842", "GSM7761842: 22 02947; Danio rerio; RNA Seq", "GSM7761842 r1", "GSM7761842", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02947_S19_L02_R1_001.fastq.gz 22-02947_S19_L02_R2_001.fastq.gz", "fastq fastq", 2634385040.0, 13440740.0, "GSM7761842 r2", "0:98 1:98", "A:699185241;C:613094915;G:611213748;T:710534569;N:356567", 98, 98, null, null, 699185241, 613094915, 611213748, 710534569, 356567, "SRX21637669", "SRS18807758", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94184, 0.93645, 0.10113, 0.10207, 0.70268, 0.70345, 0.50894, 0.50924, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26408, "SRR25917823", "SRX21637669", "SRS18807758", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02947", "GSM7761842", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing", "22 02947", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6", "GSM7761842", "GSM7761842: 22 02947; Danio rerio; RNA Seq", "GSM7761842 r1", "GSM7761842", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02947_S19_L03_R1_001.fastq.gz 22-02947_S19_L03_R2_001.fastq.gz", "fastq fastq", 2356722424.0, 12024094.0, "GSM7761842 r3", "0:98 1:98", "A:626784832;C:546121522;G:545024526;T:638243477;N:548067", 98, 98, null, null, 626784832, 546121522, 545024526, 638243477, 548067, "SRX21637669", "SRS18807758", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94068, 0.93749, 0.09906, 0.10122, 0.7039, 0.70449, 0.50662, 0.51119, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26409, "SRR25917824", "SRX21637669", "SRS18807758", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02947", "GSM7761842", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.6|geo loc name:missing|collection date:missing", "22 02947", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.6", "GSM7761842", "GSM7761842: 22 02947; Danio rerio; RNA Seq", "GSM7761842 r1", "GSM7761842", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02947_S19_L04_R1_001.fastq.gz 22-02947_S19_L04_R2_001.fastq.gz", "fastq fastq", 3824206372.0, 19511257.0, "GSM7761842 r4", "0:98 1:98", "A:1013047237;C:890237600;G:890115590;T:1030706585;N:99360", 98, 98, null, null, 1013047237, 890237600, 890115590, 1030706585, 99360, "SRX21637669", "SRS18807758", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9463, 0.94321, 0.10017, 0.1014, 0.7038, 0.70437, 0.50533, 0.51168, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26410, "SRR25917825", "SRX21637668", "SRS18807757", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02946", "GSM7761841", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing", "22 02946", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5", "GSM7761841", "GSM7761841: 22 02946; Danio rerio; RNA Seq", "GSM7761841 r1", "GSM7761841", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02946_S18_L01_R1_001.fastq.gz 22-02946_S18_L01_R2_001.fastq.gz", "fastq fastq", 2024888936.0, 10331066.0, "GSM7761841 r1", "0:98 1:98", "A:542606378;C:466454644;G:464323282;T:550429046;N:1075586", 98, 98, null, null, 542606378, 466454644, 464323282, 550429046, 1075586, "SRX21637668", "SRS18807757", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.933, 0.92706, 0.10233, 0.10303, 0.70429, 0.70465, 0.49443, 0.48878, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26411, "SRR25917826", "SRX21637668", "SRS18807757", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02946", "GSM7761841", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing", "22 02946", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5", "GSM7761841", "GSM7761841: 22 02946; Danio rerio; RNA Seq", "GSM7761841 r1", "GSM7761841", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02946_S18_L02_R1_001.fastq.gz 22-02946_S18_L02_R2_001.fastq.gz", "fastq fastq", 3069224368.0, 15659308.0, "GSM7761841 r2", "0:98 1:98", "A:816848746;C:712756904;G:710416167;T:828782508;N:420043", 98, 98, null, null, 816848746, 712756904, 710416167, 828782508, 420043, "SRX21637668", "SRS18807757", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94117, 0.93483, 0.10216, 0.10274, 0.70467, 0.7051, 0.50931, 0.51613, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26412, "SRR25917827", "SRX21637668", "SRS18807757", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02946", "GSM7761841", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing", "22 02946", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5", "GSM7761841", "GSM7761841: 22 02946; Danio rerio; RNA Seq", "GSM7761841 r1", "GSM7761841", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02946_S18_L03_R1_001.fastq.gz 22-02946_S18_L03_R2_001.fastq.gz", "fastq fastq", 2612758008.0, 13330398.0, "GSM7761841 r3", "0:98 1:98", "A:695834172;C:605270278;G:603512924;T:707518532;N:622102", 98, 98, null, null, 695834172, 605270278, 603512924, 707518532, 622102, "SRX21637668", "SRS18807757", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94095, 0.93716, 0.09929, 0.10092, 0.70343, 0.70396, 0.49363, 0.50028, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26413, "SRR25917828", "SRX21637668", "SRS18807757", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02946", "GSM7761841", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.5|geo loc name:missing|collection date:missing", "22 02946", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.5", "GSM7761841", "GSM7761841: 22 02946; Danio rerio; RNA Seq", "GSM7761841 r1", "GSM7761841", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02946_S18_L04_R1_001.fastq.gz 22-02946_S18_L04_R2_001.fastq.gz", "fastq fastq", 4163040196.0, 21240001.0, "GSM7761841 r4", "0:98 1:98", "A:1104116525;C:968916166;G:968183447;T:1121718793;N:105265", 98, 98, null, null, 1104116525, 968916166, 968183447, 1121718793, 105265, "SRX21637668", "SRS18807757", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94611, 0.94219, 0.09973, 0.10107, 0.70303, 0.70394, 0.51684, 0.51536, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26414, "SRR25917829", "SRX21637667", "SRS18807756", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02945", "GSM7761840", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing", "22 02945", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2", "GSM7761840", "GSM7761840: 22 02945; Danio rerio; RNA Seq", "GSM7761840 r1", "GSM7761840", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02945_S17_L01_R1_001.fastq.gz 22-02945_S17_L01_R2_001.fastq.gz", "fastq fastq", 2619858892.0, 13366627.0, "GSM7761840 r1", "0:98 1:98", "A:705166138;C:600115338;G:598330950;T:714861086;N:1385380", 98, 98, null, null, 705166138, 600115338, 598330950, 714861086, 1385380, "SRX21637667", "SRS18807756", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93476, 0.92831, 0.09718, 0.09862, 0.70457, 0.70567, 0.4957, 0.52808, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26415, "SRR25917830", "SRX21637667", "SRS18807756", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02945", "GSM7761840", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing", "22 02945", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2", "GSM7761840", "GSM7761840: 22 02945; Danio rerio; RNA Seq", "GSM7761840 r1", "GSM7761840", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02945_S17_L02_R1_001.fastq.gz 22-02945_S17_L02_R2_001.fastq.gz", "fastq fastq", 3955690816.0, 20182096.0, "GSM7761840 r2", "0:98 1:98", "A:1058443729;C:912805409;G:911028821;T:1072858146;N:554711", 98, 98, null, null, 1058443729, 912805409, 911028821, 1072858146, 554711, "SRX21637667", "SRS18807756", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94318, 0.93872, 0.09645, 0.0973, 0.70613, 0.70715, 0.52714, 0.52457, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26416, "SRR25917831", "SRX21637667", "SRS18807756", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02945", "GSM7761840", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing", "22 02945", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2", "GSM7761840", "GSM7761840: 22 02945; Danio rerio; RNA Seq", "GSM7761840 r1", "GSM7761840", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02945_S17_L03_R1_001.fastq.gz 22-02945_S17_L03_R2_001.fastq.gz", "fastq fastq", 3434879028.0, 17524893.0, "GSM7761840 r3", "0:98 1:98", "A:919933771;C:790247133;G:789182712;T:934693677;N:821735", 98, 98, null, null, 919933771, 790247133, 789182712, 934693677, 821735, "SRX21637667", "SRS18807756", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94324, 0.93862, 0.09659, 0.09728, 0.70571, 0.70583, 0.52686, 0.53004, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26417, "SRR25917832", "SRX21637667", "SRS18807756", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02945", "GSM7761840", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.2|geo loc name:missing|collection date:missing", "22 02945", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.2", "GSM7761840", "GSM7761840: 22 02945; Danio rerio; RNA Seq", "GSM7761840 r1", "GSM7761840", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02945_S17_L04_R1_001.fastq.gz 22-02945_S17_L04_R2_001.fastq.gz", "fastq fastq", 5433098048.0, 27719888.0, "GSM7761840 r4", "0:98 1:98", "A:1449452101;C:1255780383;G:1256728807;T:1470998035;N:138722", 98, 98, null, null, 1449452101, 1255780383, 1256728807, 1470998035, 138722, "SRX21637667", "SRS18807756", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94785, 0.94392, 0.09527, 0.09667, 0.70556, 0.70676, 0.52907, 0.52805, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26418, "SRR25917833", "SRX21637666", "SRS18807755", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02942", "GSM7761839", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02942", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6", "GSM7761839", "GSM7761839: 22 02942; Danio rerio; RNA Seq", "GSM7761839 r1", "GSM7761839", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02942_S16_L01_R1_001.fastq.gz 22-02942_S16_L01_R2_001.fastq.gz", "fastq fastq", 1924129256.0, 9816986.0, "GSM7761839 r1", "0:98 1:98", "A:513816169;C:444302395;G:442002444;T:522987233;N:1021015", 98, 98, null, null, 513816169, 444302395, 442002444, 522987233, 1021015, "SRX21637666", "SRS18807755", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93541, 0.9292, 0.09209, 0.09323, 0.70496, 0.70595, 0.50865, 0.51472, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26419, "SRR25917834", "SRX21637666", "SRS18807755", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02942", "GSM7761839", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02942", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6", "GSM7761839", "GSM7761839: 22 02942; Danio rerio; RNA Seq", "GSM7761839 r1", "GSM7761839", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02942_S16_L02_R1_001.fastq.gz 22-02942_S16_L02_R2_001.fastq.gz", "fastq fastq", 3006370892.0, 15338627.0, "GSM7761839 r2", "0:98 1:98", "A:798357725;C:699049238;G:696286354;T:812267336;N:410239", 98, 98, null, null, 798357725, 699049238, 696286354, 812267336, 410239, "SRX21637666", "SRS18807755", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94371, 0.93809, 0.09, 0.09081, 0.70429, 0.7054, 0.50485, 0.50657, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26420, "SRR25917835", "SRX21637666", "SRS18807755", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02942", "GSM7761839", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02942", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6", "GSM7761839", "GSM7761839: 22 02942; Danio rerio; RNA Seq", "GSM7761839 r1", "GSM7761839", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02942_S16_L03_R1_001.fastq.gz 22-02942_S16_L03_R2_001.fastq.gz", "fastq fastq", 2569908488.0, 13111778.0, "GSM7761839 r3", "0:98 1:98", "A:683489191;C:595497651;G:593400486;T:696913366;N:607794", 98, 98, null, null, 683489191, 595497651, 593400486, 696913366, 607794, "SRX21637666", "SRS18807755", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94243, 0.93803, 0.0901, 0.09173, 0.70601, 0.70595, 0.5082, 0.50536, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26421, "SRR25917836", "SRX21637666", "SRS18807755", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02942", "GSM7761839", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02942", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:4|rin:9.6", "GSM7761839", "GSM7761839: 22 02942; Danio rerio; RNA Seq", "GSM7761839 r1", "GSM7761839", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02942_S16_L04_R1_001.fastq.gz 22-02942_S16_L04_R2_001.fastq.gz", "fastq fastq", 4090784012.0, 20871347.0, "GSM7761839 r4", "0:98 1:98", "A:1082885031;C:953380881;G:951809866;T:1102604651;N:103583", 98, 98, null, null, 1082885031, 953380881, 951809866, 1102604651, 103583, "SRX21637666", "SRS18807755", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9483, 0.94389, 0.08825, 0.08951, 0.70575, 0.70642, 0.5123, 0.50956, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26422, "SRR25917837", "SRX21637665", "SRS18807754", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02941", "GSM7761838", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02941", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6", "GSM7761838", "GSM7761838: 22 02941; Danio rerio; RNA Seq", "GSM7761838 r1", "GSM7761838", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02941_S15_L01_R1_001.fastq.gz 22-02941_S15_L01_R2_001.fastq.gz", "fastq fastq", 1451986424.0, 7408094.0, "GSM7761838 r1", "0:98 1:98", "A:390918596;C:332118752;G:330611037;T:397580767;N:757272", 98, 98, null, null, 390918596, 332118752, 330611037, 397580767, 757272, "SRX21637665", "SRS18807754", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93162, 0.92627, 0.10255, 0.10375, 0.7067, 0.70741, 0.48748, 0.50266, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26423, "SRR25917838", "SRX21637665", "SRS18807754", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02941", "GSM7761838", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02941", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6", "GSM7761838", "GSM7761838: 22 02941; Danio rerio; RNA Seq", "GSM7761838 r1", "GSM7761838", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02941_S15_L02_R1_001.fastq.gz 22-02941_S15_L02_R2_001.fastq.gz", "fastq fastq", 2226903784.0, 11361754.0, "GSM7761838 r2", "0:98 1:98", "A:595644295;C:513538924;G:511376888;T:606030075;N:313602", 98, 98, null, null, 595644295, 513538924, 511376888, 606030075, 313602, "SRX21637665", "SRS18807754", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94004, 0.93541, 0.09921, 0.10033, 0.70374, 0.70471, 0.50851, 0.50748, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26424, "SRR25917839", "SRX21637665", "SRS18807754", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02941", "GSM7761838", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02941", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6", "GSM7761838", "GSM7761838: 22 02941; Danio rerio; RNA Seq", "GSM7761838 r1", "GSM7761838", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02941_S15_L03_R1_001.fastq.gz 22-02941_S15_L03_R2_001.fastq.gz", "fastq fastq", 1835563128.0, 9365118.0, "GSM7761838 r3", "0:98 1:98", "A:491600256;C:421963198;G:420470403;T:501084604;N:444667", 98, 98, null, null, 491600256, 421963198, 420470403, 501084604, 444667, "SRX21637665", "SRS18807754", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93909, 0.93552, 0.09787, 0.10025, 0.7063, 0.70668, 0.49667, 0.49612, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26425, "SRR25917840", "SRX21637665", "SRS18807754", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02941", "GSM7761838", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:4|rin:9.6|geo loc name:missing|collection date:missing", "22 02941", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:4|rin:9.6", "GSM7761838", "GSM7761838: 22 02941; Danio rerio; RNA Seq", "GSM7761838 r1", "GSM7761838", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02941_S15_L04_R1_001.fastq.gz 22-02941_S15_L04_R2_001.fastq.gz", "fastq fastq", 3014378668.0, 15379483.0, "GSM7761838 r4", "0:98 1:98", "A:802870126;C:697333543;G:696291116;T:817807708;N:76175", 98, 98, null, null, 802870126, 697333543, 696291116, 817807708, 76175, "SRX21637665", "SRS18807754", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94458, 0.94088, 0.0997, 0.10084, 0.70542, 0.70615, 0.49847, 0.50128, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26426, "SRR25917841", "SRX21637664", "SRS18807753", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02938", "GSM7761837", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing", "22 02938", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2", "GSM7761837", "GSM7761837: 22 02938; Danio rerio; RNA Seq", "GSM7761837 r1", "GSM7761837", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02938_S14_L01_R1_001.fastq.gz 22-02938_S14_L01_R2_001.fastq.gz", "fastq fastq", 1991261020.0, 10159495.0, "GSM7761837 r1", "0:98 1:98", "A:532249087;C:459160151;G:456558143;T:542243720;N:1049919", 98, 98, null, null, 532249087, 459160151, 456558143, 542243720, 1049919, "SRX21637664", "SRS18807753", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93301, 0.92619, 0.10156, 0.10145, 0.70203, 0.70354, 0.50217, 0.50319, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26427, "SRR25917842", "SRX21637664", "SRS18807753", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02938", "GSM7761837", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing", "22 02938", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2", "GSM7761837", "GSM7761837: 22 02938; Danio rerio; RNA Seq", "GSM7761837 r1", "GSM7761837", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02938_S14_L02_R1_001.fastq.gz 22-02938_S14_L02_R2_001.fastq.gz", "fastq fastq", 3089219896.0, 15761326.0, "GSM7761837 r2", "0:98 1:98", "A:820946080;C:717486845;G:714242053;T:836115769;N:429149", 98, 98, null, null, 820946080, 717486845, 714242053, 836115769, 429149, "SRX21637664", "SRS18807753", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93958, 0.93485, 0.09922, 0.10087, 0.70297, 0.70374, 0.48594, 0.48787, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26428, "SRR25917843", "SRX21637664", "SRS18807753", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02938", "GSM7761837", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing", "22 02938", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2", "GSM7761837", "GSM7761837: 22 02938; Danio rerio; RNA Seq", "GSM7761837 r1", "GSM7761837", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02938_S14_L03_R1_001.fastq.gz 22-02938_S14_L03_R2_001.fastq.gz", "fastq fastq", 2646575652.0, 13502937.0, "GSM7761837 r3", "0:98 1:98", "A:704124909;C:612713176;G:610276201;T:718835355;N:626011", 98, 98, null, null, 704124909, 612713176, 610276201, 718835355, 626011, "SRX21637664", "SRS18807753", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93984, 0.93514, 0.09825, 0.09978, 0.70368, 0.70364, 0.50476, 0.5062, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26429, "SRR25917844", "SRX21637664", "SRS18807753", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02938", "GSM7761837", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:3|rin:9.2|geo loc name:missing|collection date:missing", "22 02938", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:3|rin:9.2", "GSM7761837", "GSM7761837: 22 02938; Danio rerio; RNA Seq", "GSM7761837 r1", "GSM7761837", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02938_S14_L04_R1_001.fastq.gz 22-02938_S14_L04_R2_001.fastq.gz", "fastq fastq", 4235942788.0, 21611953.0, "GSM7761837 r4", "0:98 1:98", "A:1121922192;C:986087720;G:984166129;T:1143659828;N:106919", 98, 98, null, null, 1121922192, 986087720, 984166129, 1143659828, 106919, "SRX21637664", "SRS18807753", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94454, 0.94039, 0.09757, 0.09901, 0.70035, 0.70138, 0.49729, 0.48826, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26430, "SRR25917845", "SRX21637663", "SRS18807752", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02937", "GSM7761836", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing", "22 02937", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3", "GSM7761836", "GSM7761836: 22 02937; Danio rerio; RNA Seq", "GSM7761836 r1", "GSM7761836", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02937_S13_L01_R1_001.fastq.gz 22-02937_S13_L01_R2_001.fastq.gz", "fastq fastq", 1825781944.0, 9315214.0, "GSM7761836 r1", "0:98 1:98", "A:489329069;C:419397972;G:418043678;T:498054837;N:956388", 98, 98, null, null, 489329069, 419397972, 418043678, 498054837, 956388, "SRX21637663", "SRS18807752", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93216, 0.9269, 0.10415, 0.10514, 0.70696, 0.70713, 0.50133, 0.50188, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26431, "SRR25917846", "SRX21637663", "SRS18807752", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02937", "GSM7761836", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing", "22 02937", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3", "GSM7761836", "GSM7761836: 22 02937; Danio rerio; RNA Seq", "GSM7761836 r1", "GSM7761836", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02937_S13_L02_R1_001.fastq.gz 22-02937_S13_L02_R2_001.fastq.gz", "fastq fastq", 2831655708.0, 14447223.0, "GSM7761836 r2", "0:98 1:98", "A:753926233;C:655777502;G:654115498;T:767448178;N:388297", 98, 98, null, null, 753926233, 655777502, 654115498, 767448178, 388297, "SRX21637663", "SRS18807752", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93913, 0.93449, 0.10226, 0.10403, 0.70623, 0.70698, 0.50808, 0.5015, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26432, "SRR25917847", "SRX21637663", "SRS18807752", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02937", "GSM7761836", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing", "22 02937", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3", "GSM7761836", "GSM7761836: 22 02937; Danio rerio; RNA Seq", "GSM7761836 r1", "GSM7761836", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02937_S13_L03_R1_001.fastq.gz 22-02937_S13_L03_R2_001.fastq.gz", "fastq fastq", 2309829816.0, 11784846.0, "GSM7761836 r3", "0:98 1:98", "A:615504790;C:533456596;G:532490021;T:627819856;N:558553", 98, 98, null, null, 615504790, 533456596, 532490021, 627819856, 558553, "SRX21637663", "SRS18807752", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93883, 0.93641, 0.10187, 0.10383, 0.70615, 0.70593, 0.49921, 0.49159, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26433, "SRR25917848", "SRX21637663", "SRS18807752", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02937", "GSM7761836", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:3|rin:9.3|geo loc name:missing|collection date:missing", "22 02937", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:3|rin:9.3", "GSM7761836", "GSM7761836: 22 02937; Danio rerio; RNA Seq", "GSM7761836 r1", "GSM7761836", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02937_S13_L04_R1_001.fastq.gz 22-02937_S13_L04_R2_001.fastq.gz", "fastq fastq", 3731146944.0, 19036464.0, "GSM7761836 r4", "0:98 1:98", "A:989277206;C:866724233;G:866705291;T:1008347419;N:92795", 98, 98, null, null, 989277206, 866724233, 866705291, 1008347419, 92795, "SRX21637663", "SRS18807752", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9451, 0.94176, 0.10033, 0.10187, 0.70494, 0.70571, 0.49807, 0.49112, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26434, "SRR25917849", "SRX21637662", "SRS18807751", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02936", "GSM7761835", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02936", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761835", "GSM7761835: 22 02936; Danio rerio; RNA Seq", "GSM7761835 r1", "GSM7761835", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02936_S12_L01_R1_001.fastq.gz 22-02936_S12_L01_R2_001.fastq.gz", "fastq fastq", 2087585416.0, 10650946.0, "GSM7761835 r1", "0:98 1:98", "A:557206023;C:482369335;G:479442541;T:567486868;N:1080649", 98, 98, null, null, 557206023, 482369335, 479442541, 567486868, 1080649, "SRX21637662", "SRS18807751", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93131, 0.92508, 0.10425, 0.10495, 0.70715, 0.70796, 0.49956, 0.48457, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26435, "SRR25917850", "SRX21637662", "SRS18807751", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02936", "GSM7761835", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02936", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761835", "GSM7761835: 22 02936; Danio rerio; RNA Seq", "GSM7761835 r1", "GSM7761835", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02936_S12_L02_R1_001.fastq.gz 22-02936_S12_L02_R2_001.fastq.gz", "fastq fastq", 3225005756.0, 16454111.0, "GSM7761835 r2", "0:98 1:98", "A:855605850;C:750757069;G:747157352;T:871043603;N:441882", 98, 98, null, null, 855605850, 750757069, 747157352, 871043603, 441882, "SRX21637662", "SRS18807751", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93771, 0.93339, 0.10257, 0.10429, 0.70601, 0.70727, 0.50591, 0.50179, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26436, "SRR25917851", "SRX21637662", "SRS18807751", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02936", "GSM7761835", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02936", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761835", "GSM7761835: 22 02936; Danio rerio; RNA Seq", "GSM7761835 r1", "GSM7761835", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02936_S12_L03_R1_001.fastq.gz 22-02936_S12_L03_R2_001.fastq.gz", "fastq fastq", 2793582512.0, 14252972.0, "GSM7761835 r3", "0:98 1:98", "A:742243213;C:648028314;G:645258591;T:757391700;N:660694", 98, 98, null, null, 742243213, 648028314, 645258591, 757391700, 660694, "SRX21637662", "SRS18807751", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9379, 0.9345, 0.10089, 0.10292, 0.70887, 0.70907, 0.48756, 0.50559, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26437, "SRR25917852", "SRX21637662", "SRS18807751", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02936", "GSM7761835", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:3|rin:9.5|geo loc name:missing|collection date:missing", "22 02936", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:3|rin:9.5", "GSM7761835", "GSM7761835: 22 02936; Danio rerio; RNA Seq", "GSM7761835 r1", "GSM7761835", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02936_S12_L04_R1_001.fastq.gz 22-02936_S12_L04_R2_001.fastq.gz", "fastq fastq", 4412090144.0, 22510664.0, "GSM7761835 r4", "0:98 1:98", "A:1166366926;C:1029504824;G:1027522438;T:1188583356;N:112600", 98, 98, null, null, 1166366926, 1029504824, 1027522438, 1188583356, 112600, "SRX21637662", "SRS18807751", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9434, 0.94005, 0.10109, 0.10212, 0.70565, 0.70627, 0.49953, 0.49393, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26438, "SRR25917853", "SRX21637661", "SRS18807750", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02935", "GSM7761834", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing", "22 02935", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3", "GSM7761834", "GSM7761834: 22 02935; Danio rerio; RNA Seq", "GSM7761834 r1", "GSM7761834", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02935_S11_L01_R1_001.fastq.gz 22-02935_S11_L01_R2_001.fastq.gz", "fastq fastq", 1425260256.0, 7271736.0, "GSM7761834 r1", "0:98 1:98", "A:380769821;C:328986720;G:327546654;T:387200001;N:757060", 98, 98, null, null, 380769821, 328986720, 327546654, 387200001, 757060, "SRX21637661", "SRS18807750", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93263, 0.92464, 0.09384, 0.0946, 0.70145, 0.70159, 0.50261, 0.49541, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26439, "SRR25917854", "SRX21637661", "SRS18807750", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02935", "GSM7761834", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing", "22 02935", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3", "GSM7761834", "GSM7761834: 22 02935; Danio rerio; RNA Seq", "GSM7761834 r1", "GSM7761834", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02935_S11_L02_R1_001.fastq.gz 22-02935_S11_L02_R2_001.fastq.gz", "fastq fastq", 2182395712.0, 11134672.0, "GSM7761834 r2", "0:98 1:98", "A:579577501;C:507352278;G:505817817;T:589350119;N:297997", 98, 98, null, null, 579577501, 507352278, 505817817, 589350119, 297997, "SRX21637661", "SRS18807750", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94061, 0.93492, 0.09299, 0.09327, 0.69968, 0.69972, 0.50173, 0.50685, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26440, "SRR25917855", "SRX21637661", "SRS18807750", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02935", "GSM7761834", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing", "22 02935", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3", "GSM7761834", "GSM7761834: 22 02935; Danio rerio; RNA Seq", "GSM7761834 r1", "GSM7761834", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02935_S11_L03_R1_001.fastq.gz 22-02935_S11_L03_R2_001.fastq.gz", "fastq fastq", 1865940776.0, 9520106.0, "GSM7761834 r3", "0:98 1:98", "A:496030337;C:432591349;G:431482394;T:505389204;N:447492", 98, 98, null, null, 496030337, 432591349, 431482394, 505389204, 447492, "SRX21637661", "SRS18807750", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93989, 0.93593, 0.09052, 0.09217, 0.70364, 0.70408, 0.49553, 0.50339, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26441, "SRR25917856", "SRX21637661", "SRS18807750", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02935", "GSM7761834", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:2|rin:9.3|geo loc name:missing|collection date:missing", "22 02935", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:2|rin:9.3", "GSM7761834", "GSM7761834: 22 02935; Danio rerio; RNA Seq", "GSM7761834 r1", "GSM7761834", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02935_S11_L04_R1_001.fastq.gz 22-02935_S11_L04_R2_001.fastq.gz", "fastq fastq", 2911163500.0, 14852875.0, "GSM7761834 r4", "0:98 1:98", "A:770358038;C:678412695;G:678127449;T:784190944;N:74374", 98, 98, null, null, 770358038, 678412695, 678127449, 784190944, 74374, "SRX21637661", "SRS18807750", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9457, 0.94244, 0.0911, 0.09245, 0.70118, 0.70242, 0.50638, 0.51106, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26442, "SRR25917857", "SRX21637660", "SRS18807749", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02934", "GSM7761833", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02934", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761833", "GSM7761833: 22 02934; Danio rerio; RNA Seq", "GSM7761833 r1", "GSM7761833", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02934_S10_L01_R1_001.fastq.gz 22-02934_S10_L01_R2_001.fastq.gz", "fastq fastq", 1634748192.0, 8340552.0, "GSM7761833 r1", "0:98 1:98", "A:437596034;C:376561669;G:375555537;T:444177229;N:857723", 98, 98, null, null, 437596034, 376561669, 375555537, 444177229, 857723, "SRX21637660", "SRS18807749", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93351, 0.93037, 0.09754, 0.09921, 0.70386, 0.70441, 0.50777, 0.50601, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26443, "SRR25917858", "SRX21637660", "SRS18807749", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02934", "GSM7761833", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02934", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761833", "GSM7761833: 22 02934; Danio rerio; RNA Seq", "GSM7761833 r1", "GSM7761833", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02934_S10_L02_R1_001.fastq.gz 22-02934_S10_L02_R2_001.fastq.gz", "fastq fastq", 2555331184.0, 13037404.0, "GSM7761833 r2", "0:98 1:98", "A:679972731;C:592870022;G:591661544;T:690487300;N:339587", 98, 98, null, null, 679972731, 592870022, 591661544, 690487300, 339587, "SRX21637660", "SRS18807749", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94259, 0.93773, 0.09654, 0.09727, 0.70276, 0.7036, 0.51546, 0.51595, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26444, "SRR25917859", "SRX21637660", "SRS18807749", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02934", "GSM7761833", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02934", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761833", "GSM7761833: 22 02934; Danio rerio; RNA Seq", "GSM7761833 r1", "GSM7761833", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02934_S10_L03_R1_001.fastq.gz 22-02934_S10_L03_R2_001.fastq.gz", "fastq fastq", 2126669188.0, 10850353.0, "GSM7761833 r3", "0:98 1:98", "A:566657230;C:491844144;G:491125243;T:576536074;N:506497", 98, 98, null, null, 566657230, 491844144, 491125243, 576536074, 506497, "SRX21637660", "SRS18807749", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94132, 0.93954, 0.09627, 0.09813, 0.70141, 0.70207, 0.50833, 0.50945, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26445, "SRR25917860", "SRX21637660", "SRS18807749", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02934", "GSM7761833", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02934", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761833", "GSM7761833: 22 02934; Danio rerio; RNA Seq", "GSM7761833 r1", "GSM7761833", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02934_S10_L04_R1_001.fastq.gz 22-02934_S10_L04_R2_001.fastq.gz", "fastq fastq", 3389559320.0, 17293670.0, "GSM7761833 r4", "0:98 1:98", "A:899016289;C:788251756;G:788352656;T:913853588;N:85031", 98, 98, null, null, 899016289, 788251756, 788352656, 913853588, 85031, "SRX21637660", "SRS18807749", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94631, 0.94381, 0.09528, 0.0969, 0.7027, 0.70297, 0.50668, 0.51126, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26446, "SRR25917861", "SRX21637659", "SRS18807748", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02933", "GSM7761832", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing", "22 02933", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9", "GSM7761832", "GSM7761832: 22 02933; Danio rerio; RNA Seq", "GSM7761832 r1", "GSM7761832", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02933_S9_L01_R1_001.fastq.gz 22-02933_S9_L01_R2_001.fastq.gz", "fastq fastq", 1625039920.0, 8291020.0, "GSM7761832 r1", "0:98 1:98", "A:437446017;C:372483047;G:371043665;T:443213897;N:853294", 98, 98, null, null, 437446017, 372483047, 371043665, 443213897, 853294, "SRX21637659", "SRS18807748", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.92998, 0.92392, 0.10748, 0.10946, 0.70836, 0.70847, 0.48907, 0.48857, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26447, "SRR25917862", "SRX21637659", "SRS18807748", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02933", "GSM7761832", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing", "22 02933", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9", "GSM7761832", "GSM7761832: 22 02933; Danio rerio; RNA Seq", "GSM7761832 r1", "GSM7761832", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02933_S9_L02_R1_001.fastq.gz 22-02933_S9_L02_R2_001.fastq.gz", "fastq fastq", 2511173364.0, 12812109.0, "GSM7761832 r2", "0:98 1:98", "A:671571720;C:580389475;G:578546462;T:680316728;N:348979", 98, 98, null, null, 671571720, 580389475, 578546462, 680316728, 348979, "SRX21637659", "SRS18807748", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93833, 0.93295, 0.10554, 0.10659, 0.70694, 0.70725, 0.49015, 0.48342, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26448, "SRR25917863", "SRX21637659", "SRS18807748", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02933", "GSM7761832", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing", "22 02933", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9", "GSM7761832", "GSM7761832: 22 02933; Danio rerio; RNA Seq", "GSM7761832 r1", "GSM7761832", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02933_S9_L03_R1_001.fastq.gz 22-02933_S9_L03_R2_001.fastq.gz", "fastq fastq", 2142414064.0, 10930684.0, "GSM7761832 r3", "0:98 1:98", "A:573997088;C:493219654;G:491924100;T:582757555;N:515667", 98, 98, null, null, 573997088, 493219654, 491924100, 582757555, 515667, "SRX21637659", "SRS18807748", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93772, 0.93308, 0.10567, 0.10721, 0.70741, 0.70802, 0.49025, 0.49086, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26449, "SRR25917864", "SRX21637659", "SRS18807748", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02933", "GSM7761832", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:female|hometank:1|rin:9|geo loc name:missing|collection date:missing", "22 02933", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:F|hometank:1|rin:9", "GSM7761832", "GSM7761832: 22 02933; Danio rerio; RNA Seq", "GSM7761832 r1", "GSM7761832", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02933_S9_L04_R1_001.fastq.gz 22-02933_S9_L04_R2_001.fastq.gz", "fastq fastq", 3407370232.0, 17384542.0, "GSM7761832 r4", "0:98 1:98", "A:907918258;C:789555234;G:788822588;T:920987647;N:86505", 98, 98, null, null, 907918258, 789555234, 788822588, 920987647, 86505, "SRX21637659", "SRS18807748", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9434, 0.93934, 0.10586, 0.10664, 0.70597, 0.7064, 0.49476, 0.49501, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26450, "SRR25917865", "SRX21637658", "SRS18807747", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02932", "GSM7761831", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing", "22 02932", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3", "GSM7761831", "GSM7761831: 22 02932; Danio rerio; RNA Seq", "GSM7761831 r1", "GSM7761831", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02932_S8_L01_R1_001.fastq.gz 22-02932_S8_L01_R2_001.fastq.gz", "fastq fastq", 1652834484.0, 8432829.0, "GSM7761831 r1", "0:98 1:98", "A:445714221;C:377297450;G:376171010;T:452774158;N:877645", 98, 98, null, null, 445714221, 377297450, 376171010, 452774158, 877645, "SRX21637658", "SRS18807747", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.92783, 0.92405, 0.11309, 0.11435, 0.70502, 0.70516, 0.51245, 0.51191, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26451, "SRR25917866", "SRX21637658", "SRS18807747", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02932", "GSM7761831", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing", "22 02932", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3", "GSM7761831", "GSM7761831: 22 02932; Danio rerio; RNA Seq", "GSM7761831 r1", "GSM7761831", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02932_S8_L02_R1_001.fastq.gz 22-02932_S8_L02_R2_001.fastq.gz", "fastq fastq", 2483826268.0, 12672583.0, "GSM7761831 r2", "0:98 1:98", "A:666132559;C:571071547;G:570172380;T:676097026;N:352756", 98, 98, null, null, 666132559, 571071547, 570172380, 676097026, 352756, "SRX21637658", "SRS18807747", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9372, 0.93314, 0.1107, 0.11198, 0.7024, 0.70311, 0.50775, 0.49851, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26452, "SRR25917867", "SRX21637658", "SRS18807747", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02932", "GSM7761831", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing", "22 02932", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3", "GSM7761831", "GSM7761831: 22 02932; Danio rerio; RNA Seq", "GSM7761831 r1", "GSM7761831", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02932_S8_L03_R1_001.fastq.gz 22-02932_S8_L03_R2_001.fastq.gz", "fastq fastq", 2257194408.0, 11516298.0, "GSM7761831 r3", "0:98 1:98", "A:605680300;C:517703393;G:517093157;T:616181689;N:535869", 98, 98, null, null, 605680300, 517703393, 517093157, 616181689, 535869, "SRX21637658", "SRS18807747", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93599, 0.9327, 0.10967, 0.11188, 0.70421, 0.70485, 0.50619, 0.50505, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26453, "SRR25917868", "SRX21637658", "SRS18807747", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02932", "GSM7761831", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:male|hometank:1|rin:9.3|geo loc name:missing|collection date:missing", "22 02932", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:M|hometank:1|rin:9.3", "GSM7761831", "GSM7761831: 22 02932; Danio rerio; RNA Seq", "GSM7761831 r1", "GSM7761831", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02932_S8_L04_R1_001.fastq.gz 22-02932_S8_L04_R2_001.fastq.gz", "fastq fastq", 3522571388.0, 17972303.0, "GSM7761831 r4", "0:98 1:98", "A:941638147;C:811658683;G:812442792;T:956741032;N:90734", 98, 98, null, null, 941638147, 811658683, 812442792, 956741032, 90734, "SRX21637658", "SRS18807747", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94177, 0.93937, 0.11052, 0.11233, 0.70094, 0.70185, 0.50644, 0.50654, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26454, "SRR25917869", "SRX21637657", "SRS18807746", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02931", "GSM7761830", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02931", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761830", "GSM7761830: 22 02931; Danio rerio; RNA Seq", "GSM7761830 r1", "GSM7761830", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02931_S7_L01_R1_001.fastq.gz 22-02931_S7_L01_R2_001.fastq.gz", "fastq fastq", 2078034924.0, 10602219.0, "GSM7761830 r1", "0:98 1:98", "A:556960818;C:477871614;G:476758987;T:565357168;N:1086337", 98, 98, null, null, 556960818, 477871614, 476758987, 565357168, 1086337, "SRX21637657", "SRS18807746", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93055, 0.92614, 0.10155, 0.10219, 0.70238, 0.70285, 0.49809, 0.49641, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26455, "SRR25917870", "SRX21637657", "SRS18807746", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02931", "GSM7761830", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02931", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761830", "GSM7761830: 22 02931; Danio rerio; RNA Seq", "GSM7761830 r1", "GSM7761830", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02931_S7_L02_R1_001.fastq.gz 22-02931_S7_L02_R2_001.fastq.gz", "fastq fastq", 3163234592.0, 16138952.0, "GSM7761830 r2", "0:98 1:98", "A:842478174;C:733095294;G:732049286;T:855168777;N:443061", 98, 98, null, null, 842478174, 733095294, 732049286, 855168777, 443061, "SRX21637657", "SRS18807746", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93831, 0.93463, 0.10061, 0.10137, 0.70276, 0.70362, 0.48735, 0.49231, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26456, "SRR25917871", "SRX21637657", "SRS18807746", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02931", "GSM7761830", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02931", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761830", "GSM7761830: 22 02931; Danio rerio; RNA Seq", "GSM7761830 r1", "GSM7761830", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02931_S7_L03_R1_001.fastq.gz 22-02931_S7_L03_R2_001.fastq.gz", "fastq fastq", 2674741832.0, 13646642.0, "GSM7761830 r3", "0:98 1:98", "A:712547758;C:618664398;G:618024646;T:724874022;N:631008", 98, 98, null, null, 712547758, 618664398, 618024646, 724874022, 631008, "SRX21637657", "SRS18807746", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93914, 0.93649, 0.09901, 0.10101, 0.70329, 0.70309, 0.49131, 0.48443, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26457, "SRR25917872", "SRX21637657", "SRS18807746", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02931", "GSM7761830", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:1|rin:9.1|geo loc name:missing|collection date:missing", "22 02931", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:1|rin:9.1", "GSM7761830", "GSM7761830: 22 02931; Danio rerio; RNA Seq", "GSM7761830 r1", "GSM7761830", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02931_S7_L04_R1_001.fastq.gz 22-02931_S7_L04_R2_001.fastq.gz", "fastq fastq", 4163977076.0, 21244781.0, "GSM7761830 r4", "0:98 1:98", "A:1104518063;C:967955798;G:968931822;T:1122465534;N:105859", 98, 98, null, null, 1104518063, 967955798, 968931822, 1122465534, 105859, "SRX21637657", "SRS18807746", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94358, 0.94145, 0.09856, 0.0999, 0.7022, 0.7023, 0.49231, 0.49411, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26458, "SRR25917873", "SRX21637656", "SRS18807745", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02930", "GSM7761829", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02930", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5", "GSM7761829", "GSM7761829: 22 02930; Danio rerio; RNA Seq", "GSM7761829 r1", "GSM7761829", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02930_S6_L01_R1_001.fastq.gz 22-02930_S6_L01_R2_001.fastq.gz", "fastq fastq", 2183053488.0, 11138028.0, "GSM7761829 r1", "0:98 1:98", "A:587746222;C:499739594;G:498918963;T:595474490;N:1174219", 98, 98, null, null, 587746222, 499739594, 498918963, 595474490, 1174219, "SRX21637656", "SRS18807745", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93008, 0.92301, 0.10276, 0.10349, 0.70467, 0.70477, 0.50182, 0.4904, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26459, "SRR25917874", "SRX21637656", "SRS18807745", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02930", "GSM7761829", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02930", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5", "GSM7761829", "GSM7761829: 22 02930; Danio rerio; RNA Seq", "GSM7761829 r1", "GSM7761829", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02930_S6_L02_R1_001.fastq.gz 22-02930_S6_L02_R2_001.fastq.gz", "fastq fastq", 3272267236.0, 16695241.0, "GSM7761829 r2", "0:98 1:98", "A:875782986;C:754682745;G:754270029;T:887061936;N:469540", 98, 98, null, null, 875782986, 754682745, 754270029, 887061936, 469540, "SRX21637656", "SRS18807745", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93964, 0.93399, 0.10278, 0.10253, 0.70272, 0.70356, 0.50742, 0.50718, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26460, "SRR25917875", "SRX21637656", "SRS18807745", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02930", "GSM7761829", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02930", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5", "GSM7761829", "GSM7761829: 22 02930; Danio rerio; RNA Seq", "GSM7761829 r1", "GSM7761829", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02930_S6_L03_R1_001.fastq.gz 22-02930_S6_L03_R2_001.fastq.gz", "fastq fastq", 2933063560.0, 14964610.0, "GSM7761829 r3", "0:98 1:98", "A:785485812;C:674759421;G:674660900;T:797470873;N:686554", 98, 98, null, null, 785485812, 674759421, 674660900, 797470873, 686554, "SRX21637656", "SRS18807745", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93883, 0.93435, 0.09945, 0.10079, 0.70394, 0.70412, 0.49002, 0.5013, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26461, "SRR25917876", "SRX21637656", "SRS18807745", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02930", "GSM7761829", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02930", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:5|rin:9.5", "GSM7761829", "GSM7761829: 22 02930; Danio rerio; RNA Seq", "GSM7761829 r1", "GSM7761829", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02930_S6_L04_R1_001.fastq.gz 22-02930_S6_L04_R2_001.fastq.gz", "fastq fastq", 4750945136.0, 24239516.0, "GSM7761829 r4", "0:98 1:98", "A:1268488476;C:1097018233;G:1099272584;T:1286042389;N:123454", 98, 98, null, null, 1268488476, 1097018233, 1099272584, 1286042389, 123454, "SRX21637656", "SRS18807745", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94232, 0.93878, 0.09951, 0.10061, 0.70327, 0.70516, 0.50625, 0.50124, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26462, "SRR25917877", "SRX21637655", "SRS18807744", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02929", "GSM7761828", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing", "22 02929", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1", "GSM7761828", "GSM7761828: 22 02929; Danio rerio; RNA Seq", "GSM7761828 r1", "GSM7761828", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02929_S5_L01_R1_001.fastq.gz 22-02929_S5_L01_R2_001.fastq.gz", "fastq fastq", 1624362544.0, 8287564.0, "GSM7761828 r1", "0:98 1:98", "A:436056094;C:372956179;G:372275222;T:442210214;N:864835", 98, 98, null, null, 436056094, 372956179, 372275222, 442210214, 864835, "SRX21637655", "SRS18807744", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93013, 0.92347, 0.1043, 0.10462, 0.70439, 0.70496, 0.48768, 0.48699, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26463, "SRR25917878", "SRX21637655", "SRS18807744", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02929", "GSM7761828", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing", "22 02929", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1", "GSM7761828", "GSM7761828: 22 02929; Danio rerio; RNA Seq", "GSM7761828 r1", "GSM7761828", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02929_S5_L02_R1_001.fastq.gz 22-02929_S5_L02_R2_001.fastq.gz", "fastq fastq", 2437979712.0, 12438672.0, "GSM7761828 r2", "0:98 1:98", "A:650251653;C:564250362;G:563686737;T:659443371;N:347589", 98, 98, null, null, 650251653, 564250362, 563686737, 659443371, 347589, "SRX21637655", "SRS18807744", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93808, 0.93228, 0.10217, 0.10348, 0.7052, 0.70642, 0.48354, 0.49828, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26464, "SRR25917879", "SRX21637655", "SRS18807744", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02929", "GSM7761828", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing", "22 02929", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1", "GSM7761828", "GSM7761828: 22 02929; Danio rerio; RNA Seq", "GSM7761828 r1", "GSM7761828", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02929_S5_L03_R1_001.fastq.gz 22-02929_S5_L03_R2_001.fastq.gz", "fastq fastq", 2103094896.0, 10730076.0, "GSM7761828 r3", "0:98 1:98", "A:561587272;C:485245220;G:484987810;T:570768889;N:505705", 98, 98, null, null, 561587272, 485245220, 484987810, 570768889, 505705, "SRX21637655", "SRS18807744", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9374, 0.93318, 0.10153, 0.1033, 0.70283, 0.70274, 0.49345, 0.49097, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26465, "SRR25917880", "SRX21637655", "SRS18807744", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02929", "GSM7761828", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.1|geo loc name:missing|collection date:missing", "22 02929", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:5|rin:9.1", "GSM7761828", "GSM7761828: 22 02929; Danio rerio; RNA Seq", "GSM7761828 r1", "GSM7761828", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02929_S5_L04_R1_001.fastq.gz 22-02929_S5_L04_R2_001.fastq.gz", "fastq fastq", 3339247884.0, 17036979.0, "GSM7761828 r4", "0:98 1:98", "A:887185623;C:774852471;G:776222517;T:900901929;N:85344", 98, 98, null, null, 887185623, 774852471, 776222517, 900901929, 85344, "SRX21637655", "SRS18807744", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94331, 0.93927, 0.1008, 0.10184, 0.70124, 0.70116, 0.49593, 0.48864, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26466, "SRR25917881", "SRX21637654", "SRS18807743", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02928", "GSM7761827", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing", "22 02928", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3", "GSM7761827", "GSM7761827: 22 02928; Danio rerio; RNA Seq", "GSM7761827 r1", "GSM7761827", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02928_S4_L01_R1_001.fastq.gz 22-02928_S4_L01_R2_001.fastq.gz", "fastq fastq", 1820089908.0, 9286173.0, "GSM7761827 r1", "0:98 1:98", "A:489328752;C:417340608;G:416061821;T:496389968;N:968759", 98, 98, null, null, 489328752, 417340608, 416061821, 496389968, 968759, "SRX21637654", "SRS18807743", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93058, 0.92445, 0.10789, 0.10868, 0.70311, 0.70437, 0.49514, 0.49715, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26467, "SRR25917882", "SRX21637654", "SRS18807743", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02928", "GSM7761827", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing", "22 02928", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3", "GSM7761827", "GSM7761827: 22 02928; Danio rerio; RNA Seq", "GSM7761827 r1", "GSM7761827", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02928_S4_L02_R1_001.fastq.gz 22-02928_S4_L02_R2_001.fastq.gz", "fastq fastq", 2727217500.0, 13914375.0, "GSM7761827 r2", "0:98 1:98", "A:728407349;C:630438451;G:629147847;T:738834234;N:389619", 98, 98, null, null, 728407349, 630438451, 629147847, 738834234, 389619, "SRX21637654", "SRS18807743", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93908, 0.9332, 0.10555, 0.10608, 0.70266, 0.70374, 0.5047, 0.50096, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26468, "SRR25917883", "SRX21637654", "SRS18807743", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02928", "GSM7761827", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing", "22 02928", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3", "GSM7761827", "GSM7761827: 22 02928; Danio rerio; RNA Seq", "GSM7761827 r1", "GSM7761827", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02928_S4_L03_R1_001.fastq.gz 22-02928_S4_L03_R2_001.fastq.gz", "fastq fastq", 2427694416.0, 12386196.0, "GSM7761827 r3", "0:98 1:98", "A:648902248;C:559681298;G:558831926;T:659701354;N:577590", 98, 98, null, null, 648902248, 559681298, 558831926, 659701354, 577590, "SRX21637654", "SRS18807743", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93814, 0.93483, 0.10441, 0.10596, 0.7027, 0.70262, 0.49778, 0.50481, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26469, "SRR25917884", "SRX21637654", "SRS18807743", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02928", "GSM7761827", null, "source name:whole brain|tissue:whole brain|genotype:MPS IIIB|Sex:female|hometank:4|rin:7.3|geo loc name:missing|collection date:missing", "22 02928", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:MPS IIIB|Sex:F|hometank:4|rin:7.3", "GSM7761827", "GSM7761827: 22 02928; Danio rerio; RNA Seq", "GSM7761827 r1", "GSM7761827", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02928_S4_L04_R1_001.fastq.gz 22-02928_S4_L04_R2_001.fastq.gz", "fastq fastq", 3804812760.0, 19412310.0, "GSM7761827 r4", "0:98 1:98", "A:1013270293;C:880885167;G:881629294;T:1028929883;N:98123", 98, 98, null, null, 1013270293, 880885167, 881629294, 1028929883, 98123, "SRX21637654", "SRS18807743", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94321, 0.93986, 0.10365, 0.10474, 0.70228, 0.7023, 0.50249, 0.49514, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26470, "SRR25917885", "SRX21637653", "SRS18807742", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02927", "GSM7761826", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing", "22 02927", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4", "GSM7761826", "GSM7761826: 22 02927; Danio rerio; RNA Seq", "GSM7761826 r1", "GSM7761826", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02927_S3_L01_R1_001.fastq.gz 22-02927_S3_L01_R2_001.fastq.gz", "fastq fastq", 2066568336.0, 10543716.0, "GSM7761826 r1", "0:98 1:98", "A:554968443;C:474349665;G:473384034;T:562774037;N:1092157", 98, 98, null, null, 554968443, 474349665, 473384034, 562774037, 1092157, "SRX21637653", "SRS18807742", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9305, 0.92427, 0.10545, 0.10708, 0.70445, 0.70542, 0.49546, 0.49704, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26471, "SRR25917886", "SRX21637653", "SRS18807742", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02927", "GSM7761826", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing", "22 02927", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4", "GSM7761826", "GSM7761826: 22 02927; Danio rerio; RNA Seq", "GSM7761826 r1", "GSM7761826", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02927_S3_L02_R1_001.fastq.gz 22-02927_S3_L02_R2_001.fastq.gz", "fastq fastq", 3133377324.0, 15986619.0, "GSM7761826 r2", "0:98 1:98", "A:836240845;C:724796464;G:723947563;T:847954984;N:437468", 98, 98, null, null, 836240845, 724796464, 723947563, 847954984, 437468, "SRX21637653", "SRS18807742", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93854, 0.93416, 0.1047, 0.1054, 0.7026, 0.70325, 0.50612, 0.49753, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26472, "SRR25917887", "SRX21637653", "SRS18807742", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02927", "GSM7761826", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing", "22 02927", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4", "GSM7761826", "GSM7761826: 22 02927; Danio rerio; RNA Seq", "GSM7761826 r1", "GSM7761826", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02927_S3_L03_R1_001.fastq.gz 22-02927_S3_L03_R2_001.fastq.gz", "fastq fastq", 2712126480.0, 13837380.0, "GSM7761826 r3", "0:98 1:98", "A:724693867;C:625398498;G:624928471;T:736458337;N:647307", 98, 98, null, null, 724693867, 625398498, 624928471, 736458337, 647307, "SRX21637653", "SRS18807742", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93801, 0.93409, 0.1026, 0.10389, 0.70437, 0.70362, 0.49241, 0.4932, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26473, "SRR25917888", "SRX21637653", "SRS18807742", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02927", "GSM7761826", null, "source name:whole brain|tissue:whole brain|genotype:wt|Sex:male|hometank:4|rin:9.4|geo loc name:missing|collection date:missing", "22 02927", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:wt|Sex:M|hometank:4|rin:9.4", "GSM7761826", "GSM7761826: 22 02927; Danio rerio; RNA Seq", "GSM7761826 r1", "GSM7761826", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02927_S3_L04_R1_001.fastq.gz 22-02927_S3_L04_R2_001.fastq.gz", "fastq fastq", 4313396892.0, 22007127.0, "GSM7761826 r4", "0:98 1:98", "A:1147167739;C:999728613;G:1001587767;T:1164801430;N:111343", 98, 98, null, null, 1147167739, 999728613, 1001587767, 1164801430, 111343, "SRX21637653", "SRS18807742", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94284, 0.94033, 0.10365, 0.10505, 0.70372, 0.70502, 0.50217, 0.50133, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26474, "SRR25917889", "SRX21637652", "SRS18807741", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02925", "GSM7761825", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing", "22 02925", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7", "GSM7761825", "GSM7761825: 22 02925; Danio rerio; RNA Seq", "GSM7761825 r1", "GSM7761825", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02925_S2_L01_R1_001.fastq.gz 22-02925_S2_L01_R2_001.fastq.gz", "fastq fastq", 1648026212.0, 8408297.0, "GSM7761825 r1", "0:98 1:98", "A:446399368;C:374586860;G:374491332;T:451683865;N:864787", 98, 98, null, null, 446399368, 374586860, 374491332, 451683865, 864787, "SRX21637652", "SRS18807741", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.92802, 0.92032, 0.11753, 0.11787, 0.7021, 0.70187, 0.49703, 0.49712, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26475, "SRR25917890", "SRX21637652", "SRS18807741", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02925", "GSM7761825", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing", "22 02925", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7", "GSM7761825", "GSM7761825: 22 02925; Danio rerio; RNA Seq", "GSM7761825 r1", "GSM7761825", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02925_S2_L02_R1_001.fastq.gz 22-02925_S2_L02_R2_001.fastq.gz", "fastq fastq", 2515102380.0, 12832155.0, "GSM7761825 r2", "0:98 1:98", "A:677045156;C:576190894;G:576470691;T:685037037;N:358602", 98, 98, null, null, 677045156, 576190894, 576470691, 685037037, 358602, "SRX21637652", "SRS18807741", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93607, 0.93068, 0.1164, 0.11733, 0.69962, 0.70055, 0.48548, 0.48955, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26476, "SRR25917891", "SRX21637652", "SRS18807741", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02925", "GSM7761825", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing", "22 02925", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7", "GSM7761825", "GSM7761825: 22 02925; Danio rerio; RNA Seq", "GSM7761825 r1", "GSM7761825", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02925_S2_L03_R1_001.fastq.gz 22-02925_S2_L03_R2_001.fastq.gz", "fastq fastq", 2154179160.0, 10990710.0, "GSM7761825 r3", "0:98 1:98", "A:580018273;C:492429243;G:492990917;T:588225663;N:515064", 98, 98, null, null, 580018273, 492429243, 492990917, 588225663, 515064, "SRX21637652", "SRS18807741", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93587, 0.93118, 0.11365, 0.11579, 0.7023, 0.70329, 0.49574, 0.48903, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26477, "SRR25917892", "SRX21637652", "SRS18807741", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02925", "GSM7761825", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing", "22 02925", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7", "GSM7761825", "GSM7761825: 22 02925; Danio rerio; RNA Seq", "GSM7761825 r1", "GSM7761825", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02925_S2_L04_R1_001.fastq.gz 22-02925_S2_L04_R2_001.fastq.gz", "fastq fastq", 3442755288.0, 17565078.0, "GSM7761825 r4", "0:98 1:98", "A:922795011;C:791376920;G:793569039;T:934926963;N:87355", 98, 98, null, null, 922795011, 791376920, 793569039, 934926963, 87355, "SRX21637652", "SRS18807741", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94191, 0.93808, 0.1144, 0.11572, 0.69988, 0.69992, 0.49539, 0.49607, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26478, "SRR25917893", "SRX21637651", "SRS18807740", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02924", "GSM7761824", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing", "22 02924", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7", "GSM7761824", "GSM7761824: 22 02924; Danio rerio; RNA Seq", "GSM7761824 r1", "GSM7761824", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02924_S1_L01_R1_001.fastq.gz 22-02924_S1_L01_R2_001.fastq.gz", "fastq fastq", 1812771268.0, 9248833.0, "GSM7761824 r1", "0:98 1:98", "A:488778459;C:414245907;G:414681978;T:494109886;N:955038", 98, 98, null, null, 488778459, 414245907, 414681978, 494109886, 955038, "SRX21637651", "SRS18807740", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93157, 0.925, 0.10556, 0.10667, 0.70441, 0.70516, 0.49678, 0.47929, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26479, "SRR25917894", "SRX21637651", "SRS18807740", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02924", "GSM7761824", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing", "22 02924", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7", "GSM7761824", "GSM7761824: 22 02924; Danio rerio; RNA Seq", "GSM7761824 r1", "GSM7761824", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02924_S1_L02_R1_001.fastq.gz 22-02924_S1_L02_R2_001.fastq.gz", "fastq fastq", 2762531604.0, 14094549.0, "GSM7761824 r2", "0:98 1:98", "A:740219895;C:636156304;G:637302723;T:748457359;N:395323", 98, 98, null, null, 740219895, 636156304, 637302723, 748457359, 395323, "SRX21637651", "SRS18807740", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94012, 0.93368, 0.10512, 0.10532, 0.70274, 0.70325, 0.5034, 0.49161, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26480, "SRR25917895", "SRX21637651", "SRS18807740", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02924", "GSM7761824", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing", "22 02924", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7", "GSM7761824", "GSM7761824: 22 02924; Danio rerio; RNA Seq", "GSM7761824 r1", "GSM7761824", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02924_S1_L03_R1_001.fastq.gz 22-02924_S1_L03_R2_001.fastq.gz", "fastq fastq", 2426954124.0, 12382419.0, "GSM7761824 r3", "0:98 1:98", "A:651215422;C:557014101;G:558379003;T:659761146;N:584452", 98, 98, null, null, 651215422, 557014101, 558379003, 659761146, 584452, "SRX21637651", "SRS18807740", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93954, 0.93574, 0.10267, 0.10394, 0.70479, 0.70483, 0.4983, 0.49865, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [26481, "SRR25917896", "SRX21637651", "SRS18807740", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB nagluA603fs in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However important commonalities were also observed pointing to fundamental underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then the entire was euthanised by cold water shock. Each fish was genotyped then n = 8 fish per wild type EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02924", "GSM7761824", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:male|hometank:2|rin:8.7|geo loc name:missing|collection date:missing", "22 02924", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11 Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11 Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:M|hometank:2|rin:8.7", "GSM7761824", "GSM7761824: 22 02924; Danio rerio; RNA Seq", "GSM7761824 r1", "GSM7761824", "1", "RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02924_S1_L04_R1_001.fastq.gz 22-02924_S1_L04_R2_001.fastq.gz", "fastq fastq", 3812781140.0, 19452965.0, "GSM7761824 r4", "0:98 1:98", "A:1018145314;C:880117086;G:883808999;T:1030612800;N:96941", 98, 98, null, null, 1018145314, 880117086, 883808999, 1030612800, 96941, "SRX21637651", "SRS18807740", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94432, 0.94097, 0.10294, 0.1038, 0.70256, 0.70341, 0.50445, 0.50525, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "Brain", "Nervous System"], [28397, "SRR26216293", "SRX21926780", "SRS19011110", "SRP463830", "PRJNA1022392", "Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state", "GSE244310", "Transcriptome Analysis", "Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish. We chose n = 6 as according to a previous power calculation this would allow approximately 70% power to detect differentially expressed genes in zebrafish models of Alzheimer's disease. However due to smaller than expected clutch sizes and questionable purified RNA quality we were forced to use multiple families of siblings or n<6 in some analyses. For the A and B AB arm of the experiment we analysed n = 4 fish per genotype which also included 4 sgsh S387Lfs/+ fish to explore cellular processes affected in the brains of presumably unaffected carriers of MPS III mutations. For the A and C AC arm we sequenced all homozygous sgsh S387Lfs zebrafish in the family n = 7 to account for the lower number of fish with this genotype in the AB arm. For the B and C BC arm we could not obtain a large enough family in a single breeding event within our timeframe to be able to compare with the other families. Therefore we analysed fish spawned by two pairs of parents P1 and P2 both doubly heterozygous for the nagluA603fs and hgsnatG577fs mutations in a total of 3 spawning events.", null, null, null, "Brain BC WT rep11 [22 01885 S45]", "GSM7813348", null, "source name:brain|tissue:brain|home tank:P1 lay1.2|genotype:WT|Sex:female|geo loc name:missing|collection date:missing", "Brain BC WT rep11 [22 01885 S45]", "Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.", "brain", null, "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer\u2019s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", "Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.", "tissue:brain|home tank:P1 lay1.2|genotype:WT|Sex:female", "GSM7813348", "GSM7813348: Brain BC WT rep11 [22 01885 S45]; Danio rerio; RNA Seq", "GSM7813348 r1", "GSM7813348", "1", "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP463830", null, null, "22-01885_S45_R2_001.merged.fastq.gz 22-01885_S45_R1_001.merged.fastq.gz", "fastq fastq", 20434168356.0, 104255961.0, "GSM7813348 r1", "0:98 1:98", "A:5389036438;C:4758919928;G:4775862064;T:5506840669;N:3509257", 98, 98, null, null, 5389036438, 4758919928, 4775862064, 5506840669, 3509257, "SRX21926780", "SRS19011110", "SRA1723608", "The University of Adelaide", "The University of Adelaide", 2, 0.94374, 0.9373, 0.09831, 0.09986, 0.70051, 0.7012, 0.49691, 0.49749, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-29", "Adult", "Adult", "Brain", "Nervous System"], [28398, "SRR26216294", "SRX21926779", "SRS19011109", "SRP463830", "PRJNA1022392", "Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state", "GSE244310", "Transcriptome Analysis", "Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish. We chose n = 6 as according to a previous power calculation this would allow approximately 70% power to detect differentially expressed genes in zebrafish models of Alzheimer's disease. However due to smaller than expected clutch sizes and questionable purified RNA quality we were forced to use multiple families of siblings or n<6 in some analyses. For the A and B AB arm of the experiment we analysed n = 4 fish per genotype which also included 4 sgsh S387Lfs/+ fish to explore cellular processes affected in the brains of presumably unaffected carriers of MPS III mutations. For the A and C AC arm we sequenced all homozygous sgsh S387Lfs zebrafish in the family n = 7 to account for the lower number of fish with this genotype in the AB arm. For the B and C BC arm we could not obtain a large enough family in a single breeding event within our timeframe to be able to compare with the other families. Therefore we analysed fish spawned by two pairs of parents P1 and P2 both doubly heterozygous for the nagluA603fs and hgsnatG577fs mutations in a total of 3 spawning events.", null, null, null, "Brain BC WT rep10 [22 01884 S44]", "GSM7813347", null, "source name:brain|tissue:brain|home tank:P1 lay1.2|genotype:WT|Sex:female|geo loc name:missing|collection date:missing", "Brain BC WT rep10 [22 01884 S44]", "Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.", "brain", null, "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer\u2019s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", "Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.", "tissue:brain|home tank:P1 lay1.2|genotype:WT|Sex:female", "GSM7813347", "GSM7813347: Brain BC WT rep10 [22 01884 S44]; Danio rerio; RNA Seq", "GSM7813347 r1", "GSM7813347", "1", "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP463830", null, null, "22-01884_S44_R2_001.merged.fastq.gz 22-01884_S44_R1_001.merged.fastq.gz", "fastq fastq", 18009760272.0, 91886532.0, "GSM7813347 r1", "0:98 1:98", "A:4720233526;C:4238307986;G:4233288270;T:4814852918;N:3077572", 98, 98, null, null, 4720233526, 4238307986, 4233288270, 4814852918, 3077572, "SRX21926779", "SRS19011109", "SRA1723608", "The University of Adelaide", "The University of Adelaide", 2, 0.94296, 0.93818, 0.09822, 0.10014, 0.69674, 0.69808, 0.50095, 0.49564, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-29", "Adult", "Adult", "Brain", "Nervous System"], [28399, "SRR26216295", "SRX21926778", "SRS19011108", "SRP463830", "PRJNA1022392", "Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state", "GSE244310", "Transcriptome Analysis", "Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish. We chose n = 6 as according to a previous power calculation this would allow approximately 70% power to detect differentially expressed genes in zebrafish models of Alzheimer's disease. However due to smaller than expected clutch sizes and questionable purified RNA quality we were forced to use multiple families of siblings or n<6 in some analyses. For the A and B AB arm of the experiment we analysed n = 4 fish per genotype which also included 4 sgsh S387Lfs/+ fish to explore cellular processes affected in the brains of presumably unaffected carriers of MPS III mutations. For the A and C AC arm we sequenced all homozygous sgsh S387Lfs zebrafish in the family n = 7 to account for the lower number of fish with this genotype in the AB arm. For the B and C BC arm we could not obtain a large enough family in a single breeding event within our timeframe to be able to compare with the other families. Therefore we analysed fish spawned by two pairs of parents P1 and P2 both doubly heterozygous for the nagluA603fs and hgsnatG577fs mutations in a total of 3 spawning events.", null, null, null, "Brain BC MPSIIIB rep8 [22 01883 S43]", "GSM7813346", null, "source name:brain|tissue:brain|home tank:P1 lay1.2|genotype:MPSIIIB|Sex:female|geo loc name:missing|collection date:missing", "Brain BC MPSIIIB rep8 [22 01883 S43]", "Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.", "brain", null, "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer\u2019s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", "Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.", "tissue:brain|home tank:P1 lay1.2|genotype:MPSIIIB|Sex:female", "GSM7813346", "GSM7813346: Brain BC MPSIIIB rep8 [22 01883 S43]; Danio rerio; RNA Seq", "GSM7813346 r1", "GSM7813346", "1", "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP463830", null, null, "22-01883_S43_R1_001.merged.fastq.gz 22-01883_S43_R2_001.merged.fastq.gz", "fastq fastq", 17370595648.0, 88625488.0, "GSM7813346 r1", "0:98 1:98", "A:4566434950;C:4075041360;G:4075273162;T:4650852579;N:2993597", 98, 98, null, null, 4566434950, 4075041360, 4075273162, 4650852579, 2993597, "SRX21926778", "SRS19011108", "SRA1723608", "The University of Adelaide", "The University of Adelaide", 2, 0.94109, 0.93655, 0.09902, 0.10131, 0.69785, 0.69921, 0.49509, 0.49323, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-29", "Adult", "Adult", "Brain", "Nervous System"], [28400, "SRR26216296", "SRX21926777", "SRS19011106", "SRP463830", "PRJNA1022392", "Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state", "GSE244310", "Transcriptome Analysis", "Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish. We chose n = 6 as according to a previous power calculation this would allow approximately 70% power to detect differentially expressed genes in zebrafish models of Alzheimer's disease. However due to smaller than expected clutch sizes and questionable purified RNA quality we were forced to use multiple families of siblings or n<6 in some analyses. For the A and B AB arm of the experiment we analysed n = 4 fish per genotype which also included 4 sgsh S387Lfs/+ fish to explore cellular processes affected in the brains of presumably unaffected carriers of MPS III mutations. For the A and C AC arm we sequenced all homozygous sgsh S387Lfs zebrafish in the family n = 7 to account for the lower number of fish with this genotype in the AB arm. For the B and C BC arm we could not obtain a large enough family in a single breeding event within our timeframe to be able to compare with the other families. Therefore we analysed fish spawned by two pairs of parents P1 and P2 both doubly heterozygous for the nagluA603fs and hgsnatG577fs mutations in a total of 3 spawning events.", null, null, null, "Brain BC MPSIIIB rep7 [22 01882 S42]", "GSM7813345", null, "source name:brain|tissue:brain|home tank:P1 lay1.1|genotype:MPSIIIB|Sex:male|geo loc name:missing|collection date:missing", "Brain BC MPSIIIB rep7 [22 01882 S42]", "Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.", "brain", null, "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer\u2019s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", "Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.", "tissue:brain|home tank:P1 lay1.1|genotype:MPSIIIB|Sex:male", "GSM7813345", "GSM7813345: Brain BC MPSIIIB rep7 [22 01882 S42]; Danio rerio; RNA Seq", "GSM7813345 r1", "GSM7813345", "1", "Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4\u00b0C before storage at 80\u00b0C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana\u2122 miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free\u2122 DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally \u2265 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP463830", null, null, "22-01882_S42_R2_001.merged.fastq.gz 22-01882_S42_R1_001.merged.fastq.gz", "fastq fastq", 22556257808.0, 115082948.0, "GSM7813345 r1", "0:98 1:98", "A:5932142973;C:5277274711;G:5294964347;T:6047997396;N:3878381", 98, 98, null, null, 5932142973, 5277274711, 5294964347, 6047997396, 3878381, "SRX21926777", "SRS19011106", "SRA1723608", "The University of Adelaide", "The University of Adelaide", 2, 0.93651, 0.93565, 0.10798, 0.10948, 0.70337, 0.70388, 0.48941, 0.49034, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-29", "Adult", "Adult", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 188, "expanded_columns": [], "expandable_columns": 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