{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and experiment.platform = \"DNBSEQ\"", "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. 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"], [34053, "SRR31034578", "SRX26420033", "SRS22939666", "SRP539240", "PRJNA1174234", "Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A", "GSE279773", "Transcriptome Analysis", "Prior to type 2 diabetes onset \u00df cells adapt to insulin resistance through compensation\u2014a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that \u00df cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for \u00df cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible \u00df cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in \u00df cells had improved glucose tolerance compared to mice lacking DHPS in \u00df cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair \u00df cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which \u00df cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.", null, "pubmed:39832654", null, "eif5a1/2 morpholino 3", "GSM8579963", null, "source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing", "eif5a1/2 morpholino 3", "Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value", "whole body", "zebrafish were treated with morpholino and RNA was extracted 24 hours later", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "tissue:whole body|treatment:eif5a1/2 morpholino", "GSM8579963", "GSM8579963: eif5a1/2 morpholino 3; Danio rerio; RNA Seq", "GSM8579963 r1", "GSM8579963", "1", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP539240", null, null, "eIF5AMO3_1.fq.gz eIF5AMO3_2.fq.gz", "fastq fastq", 6591810600.0, 21972702.0, "GSM8579963 r1", "0:150 1:150", "A:1735827111;C:1561621052;G:1576813159;T:1717549278;N:0", 150, 150, null, null, 1735827111, 1561621052, 1576813159, 1717549278, 0, "SRX26420033", "SRS22939666", "SRA1993170", "Medicine, University of Chicago", "Medicine, University of Chicago", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [34054, "SRR31034579", "SRX26420032", "SRS22939665", "SRP539240", "PRJNA1174234", "Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A", "GSE279773", "Transcriptome Analysis", "Prior to type 2 diabetes onset \u00df cells adapt to insulin resistance through compensation\u2014a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that \u00df cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for \u00df cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible \u00df cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in \u00df cells had improved glucose tolerance compared to mice lacking DHPS in \u00df cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair \u00df cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which \u00df cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.", null, "pubmed:39832654", null, "eif5a1/2 morpholino 2", "GSM8579962", null, "source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing", "eif5a1/2 morpholino 2", "Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value", "whole body", "zebrafish were treated with morpholino and RNA was extracted 24 hours later", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "tissue:whole body|treatment:eif5a1/2 morpholino", "GSM8579962", "GSM8579962: eif5a1/2 morpholino 2; Danio rerio; RNA Seq", "GSM8579962 r1", "GSM8579962", "1", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP539240", null, null, "eIF5AMO2_1.fq.gz eIF5AMO2_2.fq.gz", "fastq fastq", 6615856500.0, 22052855.0, "GSM8579962 r1", "0:150 1:150", "A:1712890711;C:1594159797;G:1606364019;T:1702441973;N:0", 150, 150, null, null, 1712890711, 1594159797, 1606364019, 1702441973, 0, "SRX26420032", "SRS22939665", "SRA1993170", "Medicine, University of Chicago", "Medicine, University of Chicago", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [34055, "SRR31034580", "SRX26420031", "SRS22939663", "SRP539240", "PRJNA1174234", "Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A", "GSE279773", "Transcriptome Analysis", "Prior to type 2 diabetes onset \u00df cells adapt to insulin resistance through compensation\u2014a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that \u00df cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for \u00df cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible \u00df cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in \u00df cells had improved glucose tolerance compared to mice lacking DHPS in \u00df cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair \u00df cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which \u00df cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.", null, "pubmed:39832654", null, "eif5a1/2 morpholino 1", "GSM8579961", null, "source name:whole body|tissue:whole body|treatment:eif5a1/2 morpholino|geo loc name:missing|collection date:missing", "eif5a1/2 morpholino 1", "Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value", "whole body", "zebrafish were treated with morpholino and RNA was extracted 24 hours later", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "tissue:whole body|treatment:eif5a1/2 morpholino", "GSM8579961", "GSM8579961: eif5a1/2 morpholino 1; Danio rerio; RNA Seq", "GSM8579961 r1", "GSM8579961", "1", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP539240", null, null, "eIF5AMO1_1.fq.gz eIF5AMO1_2.fq.gz", "fastq fastq", 6172597200.0, 20575324.0, "GSM8579961 r1", "0:150 1:150", "A:1612632964;C:1473173555;G:1490511736;T:1596278945;N:0", 150, 150, null, null, 1612632964, 1473173555, 1490511736, 1596278945, 0, "SRX26420031", "SRS22939663", "SRA1993170", "Medicine, University of Chicago", "Medicine, University of Chicago", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Undetermined", "Embryo", "Trunk", "Surface Structure"], [34056, "SRR31034581", "SRX26420030", "SRS22939664", "SRP539240", "PRJNA1174234", "Organogenesis and replication phenoypes in vivo suggest distinct effects of hypusinated and unhypusinated eIF5A", "GSE279773", "Transcriptome Analysis", "Prior to type 2 diabetes onset \u00df cells adapt to insulin resistance through compensation\u2014a process that maintains insulin secretion and glucose homeostasis. Our lab has previously shown that \u00df cell compensation requires the activity of deoxyhypusine synthase DHPS which post translationally catalyzes the formation of the amino acid hypusine at Lys50 of eukaryotic initiation factor eIF5A. Although hypusinated eIF5A is required for \u00df cell compensation it is unclear if unhypusinated eIF5A limits this compensatory response. To identify the role of unhypusinated eIF5A we used the following animal and cell based models: transgenic zebrafish and inducible \u00df cell specific knockout mice fed a high fat diet. Zebrafish embryos injected with morpholinos to reduce global DHPS and accumulate unhypusinated eIF5A showed stunted exocrine pancreas growth at xxx dpf Although those injected with anti eIF5A morpholinos to deplete all eIF5A showed normal pancreas growth. Although a unique function of unhypusinated eIF5A has not yet been documented these findings suggest that the presence of unhypusinated eIF5A may be the major driver of altered pancreas phenotypes. Similarly following 4 weeks of high fat diet feeding and obesity mice lacking total eIF5A in \u00df cells had improved glucose tolerance compared to mice lacking DHPS in \u00df cells despite similar weight gain and insulin sensitivity. Taken together our data provide evidence that DHPS deficiency and obesity conditions impair \u00df cell function inpart from the accumulation of the unhypusinated form of eIF5A. Our studies reveal a mechanism in which \u00df cells respond to obesity by regulating mRNA translation through the balance between hypusinated and unhypusinated forms of eIF5A. Overall design: Zebrafish embryos were injected with control dhps or eif5a1/2 morpholinos; 24 hpf embryoes were processed for RNA and sent to sequencing.", null, "pubmed:39832654", null, "dhps morpholino 3", "GSM8579960", null, "source name:whole body|tissue:whole body|treatment:dhps morpholino|geo loc name:missing|collection date:missing", "dhps morpholino 3", "Data was analyzed using Dr. Tom Assembly: GRCz11 Supplementary files format and content: excel file with tpm and read counts Supplementary files format and content: excel file with fold change and q value", "whole body", "zebrafish were treated with morpholino and RNA was extracted 24 hours later", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "tissue:whole body|treatment:dhps morpholino", "GSM8579960", "GSM8579960: dhps morpholino 3; Danio rerio; RNA Seq", "GSM8579960 r1", "GSM8579960", "1", "RNA was extracted using a trizol chloroform protocol mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control. mRNA enrichment was performed on total RNA using oligodT attached magnetic beads. The enriched mRNA with polyA tails was fragmented using a fragmentation buffer followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double stranded DNA was then end repaired and five prime phosphorylated with a protruding 'A' at the three prime end forming a blunt end followed by ligation of a bubble shaped adapter with a protruding 'T' at the three primeend. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands and then single stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality checked and sequenced post passing the quality control.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP539240", null, null, "DHPSMO3_1.fq.gz DHPSMO3_2.fq.gz", "fastq fastq", 6620802600.0, 22069342.0, "GSM8579960 r1", "0:150 1:150", "A:1736599369;C:1572800715;G:1587922794;T:1723479722;N:0", 150, 150, null, null, 1736599369, 1572800715, 1587922794, 1723479722, 0, "SRX26420030", "SRS22939664", "SRA1993170", "Medicine, University of Chicago", "Medicine, University of Chicago", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "3prime", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-10-17", "Undetermined", "Embryo", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 568, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", 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