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100 rows where devstage_curation_coarse = "Undetermined" and experiment.platform = "DNBSEQ"

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experiment.library_source 2

tissue_curation_coarse 1

tissue_curation 1

technology 1

experiment.platform 1

  • DNBSEQ · 100 ✖

experiment.library_strategy 1

experiment.library_selection 1

experiment.library_layout 1

devstage_curation_coarse 1

  • Undetermined · 100 ✖

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
26386 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       22 02953 GSM7761847   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26387 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       22 02953 GSM7761847   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26388 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       22 02953 GSM7761847   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26389 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       22 02953 GSM7761847   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26390 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       22 02952 GSM7761846   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26391 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       22 02952 GSM7761846   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26392 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       22 02952 GSM7761846   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26393 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       22 02952 GSM7761846   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26394 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       22 02951 GSM7761845   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26395 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       22 02951 GSM7761845   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26396 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       22 02951 GSM7761845   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26397 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       22 02951 GSM7761845   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26398 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       22 02949 GSM7761844   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26399 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       22 02949 GSM7761844   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26400 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       22 02949 GSM7761844   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26401 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       22 02949 GSM7761844   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26402 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       22 02948 GSM7761843   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26403 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       22 02948 GSM7761843   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26404 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       22 02948 GSM7761843   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26405 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       22 02948 GSM7761843   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26406 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       22 02947 GSM7761842   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26407 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       22 02947 GSM7761842   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26408 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       22 02947 GSM7761842   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26409 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       22 02947 GSM7761842   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26410 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       22 02946 GSM7761841   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26411 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       22 02946 GSM7761841   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26412 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       22 02946 GSM7761841   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26413 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       22 02946 GSM7761841   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26414 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       22 02945 GSM7761840   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26415 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       22 02945 GSM7761840   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26416 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       22 02945 GSM7761840   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26417 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       22 02945 GSM7761840   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26418 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       22 02942 GSM7761839   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26419 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       22 02942 GSM7761839   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26420 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       22 02942 GSM7761839   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26421 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       22 02942 GSM7761839   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26422 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       22 02941 GSM7761838   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26423 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       22 02941 GSM7761838   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26424 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       22 02941 GSM7761838   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26425 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       22 02941 GSM7761838   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26426 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       22 02938 GSM7761837   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26427 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       22 02938 GSM7761837   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26428 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       22 02938 GSM7761837   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26429 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       22 02938 GSM7761837   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26430 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       22 02937 GSM7761836   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26431 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       22 02937 GSM7761836   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26432 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       22 02937 GSM7761836   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26433 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       22 02937 GSM7761836   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26434 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       22 02936 GSM7761835   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26435 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       22 02936 GSM7761835   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26436 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       22 02936 GSM7761835   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26437 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       22 02936 GSM7761835   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26438 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       22 02935 GSM7761834   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26439 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       22 02935 GSM7761834   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26440 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       22 02935 GSM7761834   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26441 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       22 02935 GSM7761834   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26442 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       22 02934 GSM7761833   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26443 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       22 02934 GSM7761833   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26444 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       22 02934 GSM7761833   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26445 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       22 02934 GSM7761833   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26446 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       22 02933 GSM7761832   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26447 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       22 02933 GSM7761832   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26448 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       22 02933 GSM7761832   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26449 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       22 02933 GSM7761832   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26450 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       22 02932 GSM7761831   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26451 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       22 02932 GSM7761831   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26452 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       22 02932 GSM7761831   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26453 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       22 02932 GSM7761831   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26454 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       22 02931 GSM7761830   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26455 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       22 02931 GSM7761830   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26456 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       22 02931 GSM7761830   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26457 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       22 02931 GSM7761830   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26458 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       22 02930 GSM7761829   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26459 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       22 02930 GSM7761829   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26460 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       22 02930 GSM7761829   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26461 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       22 02930 GSM7761829   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26462 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       22 02929 GSM7761828   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26463 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       22 02929 GSM7761828   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26464 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       22 02929 GSM7761828   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26465 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       22 02929 GSM7761828   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26466 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       22 02928 GSM7761827   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26467 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       22 02928 GSM7761827   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26468 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       22 02928 GSM7761827   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26469 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       22 02928 GSM7761827   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26470 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       22 02927 GSM7761826   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26471 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       22 02927 GSM7761826   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26472 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       22 02927 GSM7761826   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26473 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       22 02927 GSM7761826   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26474 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       22 02925 GSM7761825   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26475 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       22 02925 GSM7761825   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26476 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       22 02925 GSM7761825   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26477 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       22 02925 GSM7761825   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26478 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       22 02924 GSM7761824   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26479 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       22 02924 GSM7761824   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26480 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       22 02924 GSM7761824   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
26481 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       22 02924 GSM7761824   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   RNA was extracted using the Qiagen Rneasy mini kit then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity   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   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED DNBSEQ DNBSEQ-G400   SRP458896   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     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   Australia 2023-09-05 Undetermined Undetermined Brain Nervous System
35816 35816 SRR33052294 SRX28317427 SRS24656196 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß 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.       WT GSM8898657   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   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   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℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     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     19898122181 17423066656 16942100032 20160847006 1388830 SRX28317427 SRS24656196 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35817 35817 SRR33052295 SRX28317426 SRS24656195 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß 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.       AD5 GSM8898656   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   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   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℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     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     22736382740 20123949961 19583698932 22509389862 2212290 SRX28317426 SRS24656195 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35818 35818 SRR33052296 SRX28317425 SRS24656194 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß 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.       AD4 GSM8898655   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   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   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℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     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     11725098079 10594300338 10327407801 12138018161 1252821 SRX28317425 SRS24656194 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35819 35819 SRR33052297 SRX28317424 SRS24656193 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß 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.       AD3 GSM8898654   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   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   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℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ 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℃ 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℃ 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℃ 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℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. 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℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ 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…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     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     15920282345 14771409856 14276809765 15621229410 1556684 SRX28317424 SRS24656193 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System

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