metadata: run_metadata: 197 rows where experiment.platform = "DNBSEQ" and tissue

197 rows where experiment.platform = "DNBSEQ" and tissue_curation = "Brain"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	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
28397	28397	SRR26216293	SRX21926780	SRS19011110	SRP463830	PRJNA1022392	Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state	GSE244310	Transcriptome Analysis	Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish.…	Brain BC WT rep11 [22 01885 S45]	GSM7813348	source name:brain\|tissue:brain\|home tank:P1 lay1.2\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep11 [22 01885 S45]	Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.	brain	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer’s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.	tissue:brain\|home tank:P1 lay1.2\|genotype:WT\|Sex:female	GSM7813348	GSM7813348: Brain BC WT rep11 [22 01885 S45]; Danio rerio; RNA Seq	GSM7813348 r1	GSM7813348	1	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP463830		22-01885_S45_R2_001.merged.fastq.gz 22-01885_S45_R1_001.merged.fastq.gz	fastq fastq	20434168356.0	104255961.0	GSM7813348 r1	0:98 1:98	A:5389036438;C:4758919928;G:4775862064;T:5506840669;N:3509257	98	98	5389036438	4758919928	4775862064	5506840669	3509257	SRX21926780	SRS19011110	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.94374	0.9373	0.09831	0.09986	0.70051	0.7012	0.49691	0.49749	98	98	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2023-09-29	Adult	Adult	Brain	Nervous System
28398	28398	SRR26216294	SRX21926779	SRS19011109	SRP463830	PRJNA1022392	Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state	GSE244310	Transcriptome Analysis	Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish.…	Brain BC WT rep10 [22 01884 S44]	GSM7813347	source name:brain\|tissue:brain\|home tank:P1 lay1.2\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep10 [22 01884 S44]	Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.	brain	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer’s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.	tissue:brain\|home tank:P1 lay1.2\|genotype:WT\|Sex:female	GSM7813347	GSM7813347: Brain BC WT rep10 [22 01884 S44]; Danio rerio; RNA Seq	GSM7813347 r1	GSM7813347	1	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP463830		22-01884_S44_R2_001.merged.fastq.gz 22-01884_S44_R1_001.merged.fastq.gz	fastq fastq	18009760272.0	91886532.0	GSM7813347 r1	0:98 1:98	A:4720233526;C:4238307986;G:4233288270;T:4814852918;N:3077572	98	98	4720233526	4238307986	4233288270	4814852918	3077572	SRX21926779	SRS19011109	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.94296	0.93818	0.09822	0.10014	0.69674	0.69808	0.50095	0.49564	98	98	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2023-09-29	Adult	Adult	Brain	Nervous System
28399	28399	SRR26216295	SRX21926778	SRS19011108	SRP463830	PRJNA1022392	Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state	GSE244310	Transcriptome Analysis	Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish.…	Brain BC MPSIIIB rep8 [22 01883 S43]	GSM7813346	source name:brain\|tissue:brain\|home tank:P1 lay1.2\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep8 [22 01883 S43]	Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.	brain	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer’s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.	tissue:brain\|home tank:P1 lay1.2\|genotype:MPSIIIB\|Sex:female	GSM7813346	GSM7813346: Brain BC MPSIIIB rep8 [22 01883 S43]; Danio rerio; RNA Seq	GSM7813346 r1	GSM7813346	1	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP463830		22-01883_S43_R1_001.merged.fastq.gz 22-01883_S43_R2_001.merged.fastq.gz	fastq fastq	17370595648.0	88625488.0	GSM7813346 r1	0:98 1:98	A:4566434950;C:4075041360;G:4075273162;T:4650852579;N:2993597	98	98	4566434950	4075041360	4075273162	4650852579	2993597	SRX21926778	SRS19011108	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.94109	0.93655	0.09902	0.10131	0.69785	0.69921	0.49509	0.49323	98	98	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2023-09-29	Adult	Adult	Brain	Nervous System
28400	28400	SRR26216296	SRX21926777	SRS19011106	SRP463830	PRJNA1022392	Zebrafish models of Mucopolysaccharidosis types IIIA B & C show hyperactivity and changes in oligodendrocyte state	GSE244310	Transcriptome Analysis	Sanfilippo syndrome childhood dementia also known as mucopolysaccharidosis type III MPS III is a rare inherited lysosomal storage disorder. Subtypes of MPS III are caused by deficiencies in one of four enzymes required for degradation of the glycosaminoglycan heparan sulfate HS. An inability to degrade HS leads to progressive neurodegeneration and death in the second or third decades of life. Knowledge of MPS III pathogenesis is incomplete and no effective therapies exist. We generated the hypomorphic mutations sgshS387Lfs nagluA603Efs and hgsnatG577Sfsin the endogenous zebrafish genes orthologous to human SGSH NAGLU and HGSNAT that are loci for mutations causing MPS III subtypes MPS IIIA B and C respectively. Our models display the primary MPS III disease signature of significant brain accumulation of HS while behavioural analyses support hyperactivity phenotypes. Brain transcriptome analysis revealed changes related to lysosomal glycosaminoglycan immune system and iron homeostasis biology in all three models but also distinct differences in brain transcriptome state between models. The transcriptome analysis also indicated marked disturbance of the oligodendrocyte cell state in the brains of MPS IIIA B and C zebrafish supporting that effects on this cell type are an early and consistent characteristic of MPS III. Overall our zebrafish models recapture key characteristics of the human disease and phenotypes seen in mouse models. Our models will allow exploitation of the zebrafish's extreme fecundity and accessible anatomy to dissect the pathological mechanisms both common and divergent between the MPS IIIA B and C subtypes. Overall design: To compare brain transcriptomes in our three MPS III zebrafish lines we generated families of 2nd Filial generation zebrafish originating from G0 in crosses of parental zebrafish heterozygous for two of the MPS III mutations. We initially aimed to analyse n = 6 fish per genotype from single families of progeny from in crosses of doubly heterozygous mutant fish.…	Brain BC MPSIIIB rep7 [22 01882 S42]	GSM7813345	source name:brain\|tissue:brain\|home tank:P1 lay1.1\|genotype:MPSIIIB\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep7 [22 01882 S42]	Pre processing was performed using a custom pipeline implemented in snakemake. Briefly the raw fastq files were subjected to initial quality checks using fastQC version 0.11.9. Then adaptors were trimmed and low quality reads removed using fastp version 0.23.1. The remaining reads were aligned to the zebrafish genomes e GRCz11 Ensembl release 101 using the splice aware alignment software STAR version 2.7.0d. Aligned reads associated with the same unique molecular identifier UMI correspond to PCR duplicates generated using library preparation. These were deduplicated using the dedup function of umi tools v1.0.1. A gene level counts matrix was then generated using featureCounts version 2.0.1. Assembly: GRCz11 Ensembl release 101 Supplementary files format and content: Both processed data files counts AB.out & counts AC BC.out consist of count data in TSV format output by featureCounts software as described in the data processing section.	brain	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer’s protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	Each fish was raised until 3 month of age in a shared water circulation system. Fish were fed twice a day with dry food in the morning and live food Artermia salina in the postnoon.	tissue:brain\|home tank:P1 lay1.1\|genotype:MPSIIIB\|Sex:male	GSM7813345	GSM7813345: Brain BC MPSIIIB rep7 [22 01882 S42]; Danio rerio; RNA Seq	GSM7813345 r1	GSM7813345	1	Each family of fish was raised until 3 month of age at which time the entire family was humanely euthanised in an ice slurry. Entire heads were excised at the level of the gills and were each incubated in 600 µl of RNAlater™ Stabilization Solution Invitrogen Thermo Fisher Scientific Waltham USA overnight at 4°C before storage at 80°C until use. The tail of each fish was also removed for genomic DNA extraction and genotype determination by PCR. Total RNAs were isolated from RNAlater preserved brains using the mirVana™ miRNA Isolation Kit Ambion Life Technologies Thermo Fisher Scientific Waltham USA following the manufacturer's protocol. To remove any carried over genomic DNA during RNA purification we treated the total RNA samples with DNaseI using the DNA free™ DNA Removal Kit Invitrogen Thermo Fisher Scientific Waltham USA following the manufacturers protocol for routine DNase treatment. 500 ng of high quality total RNA with RINe generally ≥ 8 was delivered on dry ice to the South Australian Genomics Centre SAGC Adelaide Australia for preparation of stranded polyA+ libraries using Nugen Universal Plus mRNA seq NuGEN Ltd. UK. Cluster generation was performed using the Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit Part No. MGI1000004155. Then 2 x 98bp paired end sequencing was performed including 8 bp unique molecular identifiers UMIs using MGI DNBSEQ G400 chemistry MGI Tech Shenzhen China. Each of the libraries was sequenced over multiple lanes and the data from each library subsequently combined.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP463830		22-01882_S42_R2_001.merged.fastq.gz 22-01882_S42_R1_001.merged.fastq.gz	fastq fastq	22556257808.0	115082948.0	GSM7813345 r1	0:98 1:98	A:5932142973;C:5277274711;G:5294964347;T:6047997396;N:3878381	98	98	5932142973	5277274711	5294964347	6047997396	3878381	SRX21926777	SRS19011106	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93651	0.93565	0.10798	0.10948	0.70337	0.70388	0.48941	0.49034	98	98	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2023-09-29	Adult	Adult	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");;