{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"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. 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 02953", "GSM7761847", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02953", "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:9.5", "GSM7761847", "GSM7761847: 22 02953; Danio rerio; RNA Seq", "GSM7761847 r1", "GSM7761847", "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", "22-02953_S24_L01_R1_001.fastq.gz 22-02953_S24_L01_R2_001.fastq.gz", "fastq fastq", 1889616596.0, 9640901.0, "GSM7761847 r1", "0:98 1:98", "A:502776047;C:437946838;G:435110760;T:512766381;N:1016570", 98, 98, null, null, 502776047, 437946838, 435110760, 512766381, 1016570, "SRX21637674", "SRS18807763", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.9328, 0.92722, 0.09638, 0.09803, 0.70285, 0.70345, 0.50688, 0.50192, 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"], [26387, "SRR25917802", "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. 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 02953", "GSM7761847", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02953", "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:9.5", "GSM7761847", "GSM7761847: 22 02953; Danio rerio; RNA Seq", "GSM7761847 r1", "GSM7761847", "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", "22-02953_S24_L02_R1_001.fastq.gz 22-02953_S24_L02_R2_001.fastq.gz", "fastq fastq", 2862274828.0, 14603443.0, "GSM7761847 r2", "0:98 1:98", "A:757126187;C:668245308;G:664888408;T:771615407;N:399518", 98, 98, null, null, 757126187, 668245308, 664888408, 771615407, 399518, "SRX21637674", "SRS18807763", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94091, 0.93645, 0.09729, 0.09803, 0.70309, 0.7041, 0.51085, 0.50502, 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"], [26388, "SRR25917803", "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. 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 02953", "GSM7761847", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02953", "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:9.5", "GSM7761847", "GSM7761847: 22 02953; Danio rerio; RNA Seq", "GSM7761847 r1", "GSM7761847", "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", "22-02953_S24_L03_R1_001.fastq.gz 22-02953_S24_L03_R2_001.fastq.gz", "fastq fastq", 2584726676.0, 13187381.0, "GSM7761847 r3", "0:98 1:98", "A:684660799;C:601450975;G:598598564;T:699408337;N:608001", 98, 98, null, null, 684660799, 601450975, 598598564, 699408337, 608001, "SRX21637674", "SRS18807763", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94069, 0.93734, 0.09389, 0.09545, 0.70264, 0.70254, 0.49261, 0.50213, 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"], [26389, "SRR25917804", "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. 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 02953", "GSM7761847", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:5|rin:9.5|geo loc name:missing|collection date:missing", "22 02953", "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:9.5", "GSM7761847", "GSM7761847: 22 02953; Danio rerio; RNA Seq", "GSM7761847 r1", "GSM7761847", "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", "22-02953_S24_L04_R1_001.fastq.gz 22-02953_S24_L04_R2_001.fastq.gz", "fastq fastq", 4100821760.0, 20922560.0, "GSM7761847 r4", "0:98 1:98", "A:1082079470;C:958686210;G:956517599;T:1103432545;N:105936", 98, 98, null, null, 1082079470, 958686210, 956517599, 1103432545, 105936, "SRX21637674", "SRS18807763", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.94702, 0.94327, 0.09591, 0.09712, 0.70252, 0.70402, 0.51264, 0.51319, 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"], [26390, "SRR25917805", "SRX21637673", "SRS18807762", "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 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_L01_R1_001.fastq.gz 22-02952_S23_L01_R2_001.fastq.gz", "fastq fastq", 1992642428.0, 10166543.0, "GSM7761846 r1", "0:98 1:98", "A:531507040;C:460525641;G:457631907;T:541925633;N:1052207", 98, 98, null, null, 531507040, 460525641, 457631907, 541925633, 1052207, "SRX21637673", "SRS18807762", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93066, 0.92518, 0.10299, 0.10378, 0.7067, 0.70735, 0.49353, 0.49352, 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"], [26391, "SRR25917806", "SRX21637673", "SRS18807762", "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 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_L02_R1_001.fastq.gz 22-02952_S23_L02_R2_001.fastq.gz", "fastq fastq", 2995445852.0, 15282887.0, "GSM7761846 r2", "0:98 1:98", "A:793690840;C:697826413;G:694428368;T:809079956;N:420275", 98, 98, null, null, 793690840, 697826413, 694428368, 809079956, 420275, "SRX21637673", "SRS18807762", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93866, 0.93421, 0.10232, 0.10415, 0.7038, 0.70496, 0.49446, 0.49935, 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"], [26392, "SRR25917807", "SRX21637673", "SRS18807762", "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 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_L03_R1_001.fastq.gz 22-02952_S23_L03_R2_001.fastq.gz", "fastq fastq", 2558248644.0, 13052289.0, "GSM7761846 r3", "0:98 1:98", "A:678550810;C:594295508;G:591607450;T:693175940;N:618936", 98, 98, null, null, 678550810, 594295508, 591607450, 693175940, 618936, "SRX21637673", "SRS18807762", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.93834, 0.93526, 0.10036, 0.10226, 0.70443, 0.70565, 0.49418, 0.4945, 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"], [26393, "SRR25917808", "SRX21637673", "SRS18807762", "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 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"], [35816, "SRR33052294", "SRX28317427", "SRS24656196", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "WT", "GSM8898657", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "WT", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898657", "GSM8898657: WT; Danio rerio; RNA Seq", "GSM8898657 r1", "GSM8898657", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "WT_L01_read_1.fq.gz WT_L01_read_2.fq.gz", "fastq fastq", 74425524705.0, 551300183.0, "GSM8898657 r1", "0:35 1:100", "A:19898122181;C:17423066656;G:16942100032;T:20160847006;N:1388830", 35, 100, null, null, 19898122181, 17423066656, 16942100032, 20160847006, 1388830, "SRX28317427", "SRS24656196", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35817, "SRR33052295", "SRX28317426", "SRS24656195", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD5", "GSM8898656", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD5", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898656", "GSM8898656: AD5; Danio rerio; RNA Seq", "GSM8898656 r1", "GSM8898656", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD5_L01_read_1.fq.gz AD5_L01_read_2.fq.gz", "fastq fastq", 84955633785.0, 629300991.0, "GSM8898656 r1", "0:35 1:100", "A:22736382740;C:20123949961;G:19583698932;T:22509389862;N:2212290", 35, 100, null, null, 22736382740, 20123949961, 19583698932, 22509389862, 2212290, "SRX28317426", "SRS24656195", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35818, "SRR33052296", "SRX28317425", "SRS24656194", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD4", "GSM8898655", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD4", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898655", "GSM8898655: AD4; Danio rerio; RNA Seq", "GSM8898655 r1", "GSM8898655", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD4_L01_read_1.fq.gz AD4_L01_read_2.fq.gz", "fastq fastq", 44786077200.0, 331748720.0, "GSM8898655 r1", "0:35 1:100", "A:11725098079;C:10594300338;G:10327407801;T:12138018161;N:1252821", 35, 100, null, null, 11725098079, 10594300338, 10327407801, 12138018161, 1252821, "SRX28317425", "SRS24656194", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"], [35819, "SRR33052297", "SRX28317424", "SRS24656193", "SRP577565", "PRJNA1248471", "P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3\u00df Inhibitors with Anti Neurodegenerative Efficacy", "GSE294097", "Transcriptome Analysis", "Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.", null, null, null, "AD3", "GSM8898654", null, "source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing", "AD3", "Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files.", "Brain", null, "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "tissue:Brain", "GSM8898654", "GSM8898654: AD3; Danio rerio; RNA Seq", "GSM8898654 r1", "GSM8898654", "1", "Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37\u2103 for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20\u2103 before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37\u2103 for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42\u2103 using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55\u2103 for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55\u2103. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8\u00d7. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55\u2103 for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37\u2103 for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer in a total volume of 100 ml with the addition of nuclease free H2O. The reaction was then run as: 1 cycle of 95\u2103 5 minutes 13 cycles of 98\u2103 20 seconds 58\u2103 20 seconds and 72\u2103 30 seconds and 1 cycle of 72\u2103 5 minutes. PCR products were purified using the AMPure XP Beads 0.63 and 0.153 used for DNB generation and finally sequenced on MGI DNBSEQ Tx sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP577565", null, null, "AD3_L01_read_1.fq.gz AD3_L01_read_2.fq.gz", "fastq fastq", 60591288060.0, 448824356.0, "GSM8898654 r1", "0:35 1:100", "A:15920282345;C:14771409856;G:14276809765;T:15621229410;N:1556684", 35, 100, null, null, 15920282345, 14771409856, 14276809765, 15621229410, 1556684, "SRX28317424", "SRS24656193", "SRA2109204", "ShanTou University", "ShanTou University", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "mate1 technical by mapping diff", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "unknown", "unknown", null, "China", "2025-04-09", "Undetermined", "Undetermined", "Brain", "Nervous System"]], "truncated": false, "filtered_table_rows_count": 100, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "DNBSEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 96, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "cDNA", "label": "cDNA", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "DNBSEQ", "label": "DNBSEQ", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=DNBSEQ", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "Nervous System", "label": "Nervous System", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&tissue_curation_coarse=Nervous+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "Brain", "label": "Brain", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&tissue_curation=Brain", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ", "results": [{"value": "unknown", "label": "unknown", "count": 100, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=DNBSEQ&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 104.4562440001755}