metadata: run_metadata: 1,275 rows where devstage_curation_coarse = "Adult" and experiment.platform = "DNBSEQ"

1,275 rows where devstage_curation_coarse = "Adult" and experiment.platform = "DNBSEQ"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
44	44	DRR668250	DRX648352	DRS458865	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 3	Zebrafish 2wpi 3	SAMD00799623	sample name:Zebrafish 2wpi 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 25\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799623	DRX648352	RNA seq of spinal cord in zebrafish at 2wpi injured 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799623				14782516800.0	73912584.0	DRR668250	0:100 1:100	A:4058090278;C:3335994894;G:3323563782;T:4062467903;N:2399943	100	100	4058090278	3335994894	3323563782	4062467903	2399943	DRX648352	DRS458865	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
45	45	DRR668249	DRX648351	DRS458864	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 2	Zebrafish 2wpi 2	SAMD00799622	sample name:Zebrafish 2wpi 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799622	DRX648351	RNA seq of spinal cord in zebrafish at 2wpi injured 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799622				13687641800.0	68438209.0	DRR668249	0:100 1:100	A:3759784620;C:3087398782;G:3083881581;T:3754378915;N:2197902	100	100	3759784620	3087398782	3083881581	3754378915	2197902	DRX648351	DRS458864	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
46	46	DRR668248	DRX648350	DRS458863	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish 2 weeks post spinal cord injury replicate 1	Zebrafish 2wpi 1	SAMD00799621	sample name:Zebrafish 2wpi 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 14\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799621	DRX648350	RNA seq of spinal cord in zebrafish at 2wpi injured 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799621				16376197200.0	81880986.0	DRR668248	0:100 1:100	A:4485868844;C:3700974430;G:3710833937;T:4475827800;N:2692189	100	100	4485868844	3700974430	3710833937	4475827800	2692189	DRX648350	DRS458863	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
47	47	DRR668247	DRX648349	DRS458862	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 3	Zebrafish Control 3	SAMD00799620	sample name:Zebrafish Control 3\|biological replicate:3\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799620	DRX648349	RNA seq of spinal cord in zebrafish at 0wpi control 3	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799620				13377538600.0	66887693.0	DRR668247	0:100 1:100	A:3725064764;C:2973653932;G:2980883214;T:3695767890;N:2168800	100	100	3725064764	2973653932	2980883214	3695767890	2168800	DRX648349	DRS458862	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
48	48	DRR668246	DRX648348	DRS458861	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 2	Zebrafish Control 2	SAMD00799619	sample name:Zebrafish Control 2\|biological replicate:2\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2023 04 21\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799619	DRX648348	RNA seq of spinal cord in zebrafish at 0wpi control 2	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799619				14971411400.0	74857057.0	DRR668246	0:100 1:100	A:4160326445;C:3329083037;G:3329123314;T:4150453700;N:2424904	100	100	4160326445	3329083037	3329123314	4150453700	2424904	DRX648348	DRS458861	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
49	49	DRR668245	DRX648347	DRS458860	DRP012880	PRJDB18466	Comparison of spinal cord regeneration capacity in zebrafish and medaka	PRJDB18466	Other	Unlike mammals zebrafish have the remarkable ability to regenerate many tissues including the spinal cord. Medaka another model fish species has a low regenerative ability in the spinal cord. Therefore comparisons with them advantageous to revealing regeneration specific mechanisms in the spinal cord. The comparison of the spinal cord regeneration abilities of zebrafish and medaka could be a promising research field to elucidate new factors that determine spinal cord regeneration ability.	pubmed:40278963	Zebrafish Intact biological replicate 1	Zebrafish Control 1	SAMD00799618	sample name:Zebrafish Control 1\|biological replicate:1\|biomaterial provider:Center of Medical Innovation and Translational Research Osaka University\|collection date:2024 05 04\|dev stage:Adult\|geo loc name:Japan\|sex:not determined\|strain:AB Zebrafish\|tissue:Spinal cord									DNBSEQ G400 paired end sequencing of SAMD00799618	DRX648347	RNA seq of spinal cord in zebrafish at 0wpi control 1	1	Total RNA was extracted using RNeasy Micro Kit Qiagen 74104 with DNase treatment RNase Free DNase Set Qiagen 79254. Libraries were constructed from the amplified total RNA.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	DRP012880	DNBSEQ G400 paired end sequencing of SAMD00799618				13912523800.0	69562619.0	DRR668245	0:100 1:100	A:3888902049;C:3079617959;G:3075111814;T:3866655202;N:2236776	100	100	3888902049	3079617959	3075111814	3866655202	2236776	DRX648347	DRS458860	DRA020617	Osaka University	Osaka University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2025-05-12	Adult	Adult	Spinal Cord	Nervous System
25297	25297	SRR25764099	SRX21486772	SRS18719072	SRP457109	PRJNA1009810	Live tracking of basal stem cells of the epidermis during growth homeostasis and injury response in zebrafish	GSE241757	Transcriptome Analysis	Basal stem cells of the epidermis continuously differentiate into keratinocytes and replenish themselves via self renewal to maintain skin homeostasis. Numerous studies have attempted to reveal how basal cells undergo differentiation or self renewal; however this has been hampered by a lack of robust basal cell markers and analytical platforms that allow single cell tracking. Here we report integrin b4 itgb4 is a useful marker for basal cell labelling irrespective of the body region stage and regenerative status. We employed Cre loxP recombination in combination with live cell tracking of single basal clones in the caudal fin and investigated the embryonic origin and behaviour of basal cells during fish growth and homeostasis. Although most basal cells including those in fins became quiescent in the adult stage genetic cell ablation showed that basal cells were reactivated to either self renew or differentiate depending on the injured cell type. Our findings provide a platform for quantitative in vivo imaging of basal stem cells applicable at wider stages and under various conditions and reveal unanticipated basal cell dynamism in response to distinct wound signals. Overall design: To investigate whether itgb4+ epidermal basal precursors already possess a basal cell like identity immediately post fate segregation at 1 dpf dpf we isolated itgb4+ basal precursors krt4+ periderm cells from zebrafish embryos at 1 dpf and adult itgb4+ basal cells from zebrafish caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells at 2 time points. Comparative gene expression profiling analysis of RNA seq data for embryonic basal cell precursors embryonic periderm and adult basal cells.	pubmed:38265193		Adult itgb4+ basal cells	GSM7734879	tissue:epidermal cells\|cell type:adult fin epidermal basal cells\|genotype:Tgitgb4:mcherry\|geo loc name:missing\|collection date:missing	Adult itgb4+ basal cells	High quality reads were mapped using hisat2 ver. 2.2.1 Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraxction and normalization were performed using featureCounts ver. 2.0.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes basic gene information gene id length Genebank id RNA type gene name product raw count RPKM and TPM values.	epidermal cells	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	cell type:adult fin epidermal basal cells\|genotype:Tgitgb4:mcherry	GSM7734879	GSM7734879: Adult itgb4+ basal cells; Danio rerio; RNA Seq	GSM7734879 r1	GSM7734879	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP457109			Adult_itgb4mcherry_S230_R1_001.fastq.gz Adult_itgb4mcherry_S230_R2_001.fastq.gz	fastq fastq	5035430000.0	12588575.0	GSM7734879 r1	0:200 1:200	A:1339392170;C:1117195164;G:1254708952;T:1323174485;N:959229	200	200	1339392170	1117195164	1254708952	1323174485	959229	SRX21486772	SRS18719072	SRA1700438	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami Lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01543	0.02468	0.00098	0.00102	0.99318	0.99387	0.47878	0.31718	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-08-28	Adult	Adult	Skin	Surface Structure
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
28401	28401	SRR26216297	SRX21926776	SRS19011107	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 rep6 [22 01881 S41]	GSM7813344	source name:brain\|tissue:brain\|home tank:P1 lay1.1\|genotype:MPSIIIB\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep6 [22 01881 S41]	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	GSM7813344	GSM7813344: Brain BC MPSIIIB rep6 [22 01881 S41]; Danio rerio; RNA Seq	GSM7813344 r1	GSM7813344	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			22-01881_S41_R2_001.merged.fastq.gz 22-01881_S41_R1_001.merged.fastq.gz	fastq fastq	13544867140.0	69106465.0	GSM7813344 r1	0:98 1:98	A:3593957976;C:3143252317;G:3143192820;T:3662150851;N:2313176	98	98	3593957976	3143252317	3143192820	3662150851	2313176	SRX21926776	SRS19011107	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.94189	0.93615	0.09975	0.10129	0.70195	0.70307	0.5056	0.505	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
28402	28402	SRR26216298	SRX21926775	SRS19011105	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 rep3 [22 01862 S24]	GSM7813327	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.1\|genotype:MPSIIIB\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep3 [22 01862 S24]	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:P2 lay3 tank2.1\|genotype:MPSIIIB\|Sex:male	GSM7813327	GSM7813327: Brain BC MPSIIIB rep3 [22 01862 S24]; Danio rerio; RNA Seq	GSM7813327 r1	GSM7813327	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			22-01862_S24_R1_001.merged.fastq.gz 22-01862_S24_R2_001.merged.fastq.gz	fastq fastq	16452824668.0	83942983.0	GSM7813327 r1	0:98 1:98	A:4477559720;C:3648309090;G:3661532584;T:4662575737;N:2847537	98	98	4477559720	3648309090	3661532584	4662575737	2847537	SRX21926775	SRS19011105	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91104	0.91207	0.18247	0.18984	0.70463	0.70309	0.48379	0.4869	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
28403	28403	SRR26216299	SRX21926774	SRS19011104	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 MPSIIIC rep1 [22 01861 S23]	GSM7813326	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.1\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep1 [22 01861 S23]	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:P2 lay3 tank2.1\|genotype:MPSIIIC\|Sex:male	GSM7813326	GSM7813326: Brain BC MPSIIIC rep1 [22 01861 S23]; Danio rerio; RNA Seq	GSM7813326 r1	GSM7813326	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			22-01861_S23_R1_001.merged.fastq.gz 22-01861_S23_R2_001.merged.fastq.gz	fastq fastq	15049678112.0	76784072.0	GSM7813326 r1	0:98 1:98	A:4184698968;C:3230678326;G:3246295686;T:4385460926;N:2544206	98	98	4184698968	3230678326	3246295686	4385460926	2544206	SRX21926774	SRS19011104	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.8935	0.9026	0.2241	0.23699	0.70707	0.70311	0.48218	0.48558	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
28404	28404	SRR26216300	SRX21926773	SRS19011103	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 rep2 [22 01860 S22]	GSM7813325	source name:brain\|tissue:brain\|home tank:P2 lay1 tank1\|genotype:MPSIIIB\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep2 [22 01860 S22]	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:P2 lay1 tank1\|genotype:MPSIIIB\|Sex:male	GSM7813325	GSM7813325: Brain BC MPSIIIB rep2 [22 01860 S22]; Danio rerio; RNA Seq	GSM7813325 r1	GSM7813325	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			22-01860_S22_R2_001.merged.fastq.gz 22-01860_S22_R1_001.merged.fastq.gz	fastq fastq	12822405456.0	65420436.0	GSM7813325 r1	0:98 1:98	A:3468590749;C:2881037791;G:2902765490;T:3567850437;N:2160989	98	98	3468590749	2881037791	2902765490	3567850437	2160989	SRX21926773	SRS19011103	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90916	0.92042	0.1609	0.17347	0.70561	0.70313	0.48953	0.48767	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
28405	28405	SRR26216301	SRX21926772	SRS19011102	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 rep1 [22 01859 S21]	GSM7813324	source name:brain\|tissue:brain\|home tank:P2 lay3 tank1\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep1 [22 01859 S21]	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:P2 lay3 tank1\|genotype:MPSIIIB\|Sex:female	GSM7813324	GSM7813324: Brain BC MPSIIIB rep1 [22 01859 S21]; Danio rerio; RNA Seq	GSM7813324 r1	GSM7813324	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			22-01859_S21_R1_001.merged.fastq.gz 22-01859_S21_R2_001.merged.fastq.gz	fastq fastq	13719489420.0	69997395.0	GSM7813324 r1	0:98 1:98	A:3755751512;C:3014995385;G:3035398792;T:3910996480;N:2347251	98	98	3755751512	3014995385	3035398792	3910996480	2347251	SRX21926772	SRS19011102	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90744	0.9116	0.20528	0.21455	0.70364	0.70153	0.49418	0.49312	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
28406	28406	SRR26216302	SRX21926771	SRS19011101	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 AC MPSIIIC rep6 [22 01858 S20]	GSM7813323	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank5\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep6 [22 01858 S20]	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:AC P2 lay1 tank5\|genotype:MPSIIIC\|Sex:male	GSM7813323	GSM7813323: Brain AC MPSIIIC rep6 [22 01858 S20]; Danio rerio; RNA Seq	GSM7813323 r1	GSM7813323	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			22-01858_S20_R2_001.merged.fastq.gz 22-01858_S20_R1_001.merged.fastq.gz	fastq fastq	15310607816.0	78115346.0	GSM7813323 r1	0:98 1:98	A:4165340199;C:3454649027;G:3451450322;T:4236592701;N:2575567	98	98	4165340199	3454649027	3451450322	4236592701	2575567	SRX21926771	SRS19011101	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92444	0.92137	0.18296	0.18603	0.70017	0.70061	0.48135	0.4834	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
28407	28407	SRR26216303	SRX21926770	SRS19011100	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 AC MPSIIIC rep5 [22 01857 S19]	GSM7813322	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank5\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep5 [22 01857 S19]	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:AC P2 lay1 tank5\|genotype:MPSIIIC\|Sex:male	GSM7813322	GSM7813322: Brain AC MPSIIIC rep5 [22 01857 S19]; Danio rerio; RNA Seq	GSM7813322 r1	GSM7813322	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			22-01857_S19_R1_001.merged.fastq.gz 22-01857_S19_R2_001.merged.fastq.gz	fastq fastq	13226432604.0	67481799.0	GSM7813322 r1	0:98 1:98	A:3542509388;C:3031510779;G:3045645724;T:3604459613;N:2307100	98	98	3542509388	3031510779	3045645724	3604459613	2307100	SRX21926770	SRS19011100	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93408	0.92841	0.13142	0.13298	0.70816	0.70826	0.49404	0.49271	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
28408	28408	SRR26216304	SRX21926769	SRS19011099	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 AC WT rep7 [22 01856 S18]	GSM7813321	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank5\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC WT rep7 [22 01856 S18]	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:AC P2 lay1 tank5\|genotype:WT\|Sex:male	GSM7813321	GSM7813321: Brain AC WT rep7 [22 01856 S18]; Danio rerio; RNA Seq	GSM7813321 r1	GSM7813321	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			22-01856_S18_R1_001.merged.fastq.gz 22-01856_S18_R2_001.merged.fastq.gz	fastq fastq	20503339304.0	104608874.0	GSM7813321 r1	0:98 1:98	A:5528898139;C:4659501597;G:4659355396;T:5652075850;N:3508322	98	98	5528898139	4659501597	4659355396	5652075850	3508322	SRX21926769	SRS19011099	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92682	0.92364	0.16389	0.16778	0.70096	0.70112	0.4854	0.48333	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
28409	28409	SRR26216305	SRX21926768	SRS19011098	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 AC MPSIIIA rep7 [22 01855 S17]	GSM7813320	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank5\|genotype:MPSIIIA\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep7 [22 01855 S17]	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:AC P2 lay1 tank5\|genotype:MPSIIIA\|Sex:male	GSM7813320	GSM7813320: Brain AC MPSIIIA rep7 [22 01855 S17]; Danio rerio; RNA Seq	GSM7813320 r1	GSM7813320	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			22-01855_S17_R1_001.merged.fastq.gz 22-01855_S17_R2_001.merged.fastq.gz	fastq fastq	19394559856.0	98951836.0	GSM7813320 r1	0:98 1:98	A:5289871689;C:4352372013;G:4340663511;T:5408322812;N:3329831	98	98	5289871689	4352372013	4340663511	5408322812	3329831	SRX21926768	SRS19011098	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92046	0.92135	0.17988	0.18544	0.70157	0.7011	0.49298	0.48867	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
28410	28410	SRR26216306	SRX21926767	SRS19011097	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 AC WT rep6 [22 01854 S16]	GSM7813319	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank4\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC WT rep6 [22 01854 S16]	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:AC P2 lay1 tank4\|genotype:WT\|Sex:male	GSM7813319	GSM7813319: Brain AC WT rep6 [22 01854 S16]; Danio rerio; RNA Seq	GSM7813319 r1	GSM7813319	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			22-01854_S16_R1_001.merged.fastq.gz 22-01854_S16_R2_001.merged.fastq.gz	fastq fastq	16294765956.0	83136561.0	GSM7813319 r1	0:98 1:98	A:4363489648;C:3732286771;G:3728959754;T:4467240758;N:2789025	98	98	4363489648	3732286771	3728959754	4467240758	2789025	SRX21926767	SRS19011097	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93124	0.92636	0.14699	0.14912	0.6999	0.69964	0.48136	0.47855	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
28411	28411	SRR26216307	SRX21926766	SRS19011096	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 AC WT rep5 [22 01853 S15]	GSM7813318	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank4\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC WT rep5 [22 01853 S15]	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:AC P2 lay1 tank4\|genotype:WT\|Sex:female	GSM7813318	GSM7813318: Brain AC WT rep5 [22 01853 S15]; Danio rerio; RNA Seq	GSM7813318 r1	GSM7813318	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			22-01853_S15_R2_001.merged.fastq.gz 22-01853_S15_R1_001.merged.fastq.gz	fastq fastq	20409440996.0	104129801.0	GSM7813318 r1	0:98 1:98	A:5486026796;C:4642485802;G:4659975719;T:5617468124;N:3484555	98	98	5486026796	4642485802	4659975719	5617468124	3484555	SRX21926766	SRS19011096	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.9275	0.92451	0.15776	0.16157	0.70682	0.7065	0.48261	0.48684	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
28412	28412	SRR26216308	SRX21926765	SRS19011095	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 AC MPSIIIA rep6 [22 01852 S14]	GSM7813317	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank4\|genotype:MPSIIIA\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep6 [22 01852 S14]	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:AC P2 lay1 tank4\|genotype:MPSIIIA\|Sex:male	GSM7813317	GSM7813317: Brain AC MPSIIIA rep6 [22 01852 S14]; Danio rerio; RNA Seq	GSM7813317 r1	GSM7813317	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			22-01852_S14_R1_001.merged.fastq.gz 22-01852_S14_R2_001.merged.fastq.gz	fastq fastq	17445291444.0	89006589.0	GSM7813317 r1	0:98 1:98	A:4748102103;C:3888877889;G:3908613563;T:4896710898;N:2986991	98	98	4748102103	3888877889	3908613563	4896710898	2986991	SRX21926765	SRS19011095	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91763	0.9177	0.18209	0.18808	0.70278	0.70147	0.48372	0.48072	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
28413	28413	SRR26216309	SRX21926764	SRS19011094	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 AC MPSIIIA rep5 [22 01851 S13]	GSM7813316	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank3\|genotype:MPSIIIA\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep5 [22 01851 S13]	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:AC P2 lay1 tank3\|genotype:MPSIIIA\|Sex:male	GSM7813316	GSM7813316: Brain AC MPSIIIA rep5 [22 01851 S13]; Danio rerio; RNA Seq	GSM7813316 r1	GSM7813316	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			22-01851_S13_R1_001.merged.fastq.gz 22-01851_S13_R2_001.merged.fastq.gz	fastq fastq	21121699116.0	107763771.0	GSM7813316 r1	0:98 1:98	A:5723207150;C:4754780028;G:4777942447;T:5862189785;N:3579706	98	98	5723207150	4754780028	4777942447	5862189785	3579706	SRX21926764	SRS19011094	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92295	0.92126	0.1654	0.17001	0.7037	0.70335	0.49469	0.49631	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
28414	28414	SRR26216310	SRX21926763	SRS19011093	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 AC WT rep4 [22 01850 S12]	GSM7813315	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank3\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC WT rep4 [22 01850 S12]	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:AC P2 lay1 tank3\|genotype:WT\|Sex:female	GSM7813315	GSM7813315: Brain AC WT rep4 [22 01850 S12]; Danio rerio; RNA Seq	GSM7813315 r1	GSM7813315	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			22-01850_S12_R1_001.merged.fastq.gz 22-01850_S12_R2_001.merged.fastq.gz	fastq fastq	14970865532.0	76381967.0	GSM7813315 r1	0:98 1:98	A:4034135351;C:3397406994;G:3405648099;T:4131112485;N:2562603	98	98	4034135351	3397406994	3405648099	4131112485	2562603	SRX21926763	SRS19011093	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92279	0.92064	0.16643	0.17092	0.70402	0.70418	0.48212	0.48221	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
28415	28415	SRR26216311	SRX21926762	SRS19011092	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 AC WT rep3 [22 01849 S11]	GSM7813314	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank3\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC WT rep3 [22 01849 S11]	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:AC P2 lay1 tank3\|genotype:WT\|Sex:male	GSM7813314	GSM7813314: Brain AC WT rep3 [22 01849 S11]; Danio rerio; RNA Seq	GSM7813314 r1	GSM7813314	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			22-01849_S11_R1_001.merged.fastq.gz 22-01849_S11_R2_001.merged.fastq.gz	fastq fastq	13483949164.0	68795659.0	GSM7813314 r1	0:98 1:98	A:3631909201;C:3062376139;G:3075381714;T:3711984954;N:2297156	98	98	3631909201	3062376139	3075381714	3711984954	2297156	SRX21926762	SRS19011092	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92694	0.92533	0.16165	0.16577	0.70688	0.70745	0.48712	0.48231	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
28416	28416	SRR26216312	SRX21926761	SRS19011091	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 AC MPSIIIC rep4 [22 01848 S10]	GSM7813313	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank3\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep4 [22 01848 S10]	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:AC P2 lay1 tank3\|genotype:MPSIIIC\|Sex:male	GSM7813313	GSM7813313: Brain AC MPSIIIC rep4 [22 01848 S10]; Danio rerio; RNA Seq	GSM7813313 r1	GSM7813313	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			22-01848_S10_R1_001.merged.fastq.gz 22-01848_S10_R2_001.merged.fastq.gz	fastq fastq	11196327520.0	57124120.0	GSM7813313 r1	0:98 1:98	A:3039336227;C:2518474505;G:2535218436;T:3101406136;N:1892216	98	98	3039336227	2518474505	2535218436	3101406136	1892216	SRX21926761	SRS19011091	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92351	0.9222	0.15807	0.16264	0.70924	0.70916	0.48542	0.49384	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
28417	28417	SRR26216313	SRX21926760	SRS19011090	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 AC MPSIIIC rep3 [22 01847 S9]	GSM7813312	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank6\|genotype:MPSIIIC\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep3 [22 01847 S9]	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:AC P2 lay1 tank6\|genotype:MPSIIIC\|Sex:female	GSM7813312	GSM7813312: Brain AC MPSIIIC rep3 [22 01847 S9]; Danio rerio; RNA Seq	GSM7813312 r1	GSM7813312	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			22-01847_S9_R1_001.merged.fastq.gz 22-01847_S9_R2_001.merged.fastq.gz	fastq fastq	18631162788.0	95056953.0	GSM7813312 r1	0:98 1:98	A:5031487220;C:4206022334;G:4219973839;T:5170494547;N:3184848	98	98	5031487220	4206022334	4219973839	5170494547	3184848	SRX21926760	SRS19011090	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92274	0.92264	0.16323	0.16972	0.70538	0.70449	0.48765	0.48719	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
28418	28418	SRR26216314	SRX21926759	SRS19011089	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 AB WT rep4 [22 00160 S16]	GSM7813303	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB WT rep4 [22 00160 S16]	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:AB P1 lay1 tank3\|genotype:WT\|Sex:female	GSM7813303	GSM7813303: Brain AB WT rep4 [22 00160 S16]; Danio rerio; RNA Seq	GSM7813303 r1	GSM7813303	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			22-00160_S16_R1_001.merged.fastq.gz 22-00160_S16_R2_001.merged.fastq.gz	fastq fastq	19648243636.0	100246141.0	GSM7813303 r1	0:98 1:98	A:5325999167;C:4367508008;G:4409495594;T:5538729015;N:6511852	98	98	5325999167	4367508008	4409495594	5538729015	6511852	SRX21926759	SRS19011089	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91143	0.91395	0.18214	0.20284	0.70175	0.69901	0.4973	0.49726	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
28419	28419	SRR26216315	SRX21926758	SRS19011088	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 AB MPSIIIB rep4 [22 00159 S15]	GSM7813302	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIB rep4 [22 00159 S15]	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:AB P1 lay1 tank3\|genotype:MPSIIIB\|Sex:female	GSM7813302	GSM7813302: Brain AB MPSIIIB rep4 [22 00159 S15]; Danio rerio; RNA Seq	GSM7813302 r1	GSM7813302	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			22-00159_S15_R1_001.merged.fastq.gz 22-00159_S15_R2_001.merged.fastq.gz	fastq fastq	21499917376.0	109693456.0	GSM7813302 r1	0:98 1:98	A:5745647949;C:4893192375;G:4930514968;T:5923547766;N:7014318	98	98	5745647949	4893192375	4930514968	5923547766	7014318	SRX21926758	SRS19011088	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92648	0.92654	0.15109	0.16305	0.70059	0.70037	0.49317	0.48848	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
28420	28420	SRR26216316	SRX21926757	SRS19011087	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 AB sgsh het rep4 [22 00158 S14]	GSM7813301	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:sgsh het\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB sgsh het rep4 [22 00158 S14]	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:AB P1 lay1 tank3\|genotype:sgsh het\|Sex:female	GSM7813301	GSM7813301: Brain AB sgsh het rep4 [22 00158 S14]; Danio rerio; RNA Seq	GSM7813301 r1	GSM7813301	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			22-00158_S14_R1_001.merged.fastq.gz 22-00158_S14_R2_001.merged.fastq.gz	fastq fastq	22230319412.0	113419997.0	GSM7813301 r1	0:98 1:98	A:6130721912;C:4821098792;G:4876843039;T:6394368688;N:7286981	98	98	6130721912	4821098792	4876843039	6394368688	7286981	SRX21926757	SRS19011087	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90557	0.91073	0.20914	0.23456	0.71155	0.70723	0.49955	0.4974	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
28421	28421	SRR26216317	SRX21926756	SRS19011086	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 AB MPSIIIA rep4 [22 00157 S13]	GSM7813300	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIA rep4 [22 00157 S13]	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:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female	GSM7813300	GSM7813300: Brain AB MPSIIIA rep4 [22 00157 S13]; Danio rerio; RNA Seq	GSM7813300 r1	GSM7813300	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			22-00157_S13_R2_001.merged.fastq.gz 22-00157_S13_R1_001.merged.fastq.gz	fastq fastq	22546811588.0	115034753.0	GSM7813300 r1	0:98 1:98	A:6142967085;C:4991190165;G:5035361097;T:6369886796;N:7406445	98	98	6142967085	4991190165	5035361097	6369886796	7406445	SRX21926756	SRS19011086	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91532	0.91952	0.18459	0.20386	0.70707	0.70666	0.49308	0.49332	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
28422	28422	SRR26216318	SRX21926755	SRS19011085	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 AB MPSIIIA rep3 [22 00156 S12]	GSM7813299	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIA rep3 [22 00156 S12]	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:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female	GSM7813299	GSM7813299: Brain AB MPSIIIA rep3 [22 00156 S12]; Danio rerio; RNA Seq	GSM7813299 r1	GSM7813299	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			22-00156_S12_R2_001.merged.fastq.gz 22-00156_S12_R1_001.merged.fastq.gz	fastq fastq	21659471372.0	110507507.0	GSM7813299 r1	0:98 1:98	A:5967042457;C:4685520941;G:4732611066;T:6267172239;N:7124669	98	98	5967042457	4685520941	4732611066	6267172239	7124669	SRX21926755	SRS19011085	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90281	0.90971	0.22168	0.25011	0.7027	0.6994	0.48627	0.48623	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
28423	28423	SRR26216319	SRX21926754	SRS19011084	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 AB MPSIIIB rep3 [22 00155 S11]	GSM7813298	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIB rep3 [22 00155 S11]	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:AB P1 lay1 tank3\|genotype:MPSIIIB\|Sex:female	GSM7813298	GSM7813298: Brain AB MPSIIIB rep3 [22 00155 S11]; Danio rerio; RNA Seq	GSM7813298 r1	GSM7813298	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			22-00155_S11_R2_001.merged.fastq.gz 22-00155_S11_R1_001.merged.fastq.gz	fastq fastq	22973518092.0	117211827.0	GSM7813298 r1	0:98 1:98	A:6205640622;C:5145809555;G:5198001598;T:6416628989;N:7437328	98	98	6205640622	5145809555	5198001598	6416628989	7437328	SRX21926754	SRS19011084	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91842	0.92237	0.17436	0.19254	0.69883	0.69834	0.49394	0.49304	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
28424	28424	SRR26216320	SRX21926753	SRS19011083	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 AB sgsh het rep3 [22 00154 S10]	GSM7813297	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:sgsh het\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB sgsh het rep3 [22 00154 S10]	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:AB P1 lay1 tank3\|genotype:sgsh het\|Sex:female	GSM7813297	GSM7813297: Brain AB sgsh het rep3 [22 00154 S10]; Danio rerio; RNA Seq	GSM7813297 r1	GSM7813297	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			22-00154_S10_R1_001.merged.fastq.gz 22-00154_S10_R2_001.merged.fastq.gz	fastq fastq	21605437896.0	110231826.0	GSM7813297 r1	0:98 1:98	A:5873646278;C:4818397053;G:4875408993;T:6030978522;N:7007050	98	98	5873646278	4818397053	4875408993	6030978522	7007050	SRX21926753	SRS19011083	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91754	0.9191	0.1734	0.18936	0.70863	0.70853	0.49545	0.49342	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
28425	28425	SRR26216321	SRX21926752	SRS19011082	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 AB MPSIIIB rep2 [22 00153 S9]	GSM7813296	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIB rep2 [22 00153 S9]	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:AB P1 lay1 tank2\|genotype:MPSIIIB\|Sex:female	GSM7813296	GSM7813296: Brain AB MPSIIIB rep2 [22 00153 S9]; Danio rerio; RNA Seq	GSM7813296 r1	GSM7813296	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			22-00153_S9_R1_001.merged.fastq.gz 22-00153_S9_R2_001.merged.fastq.gz	fastq fastq	20290379816.0	103522346.0	GSM7813296 r1	0:98 1:98	A:5512611544;C:4506159259;G:4545779658;T:5719122488;N:6706867	98	98	5512611544	4506159259	4545779658	5719122488	6706867	SRX21926752	SRS19011082	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91537	0.92019	0.18133	0.20302	0.70205	0.69929	0.49316	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
28426	28426	SRR26216322	SRX21926751	SRS19011081	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 rep9 [22 01879 S40]	GSM7813343	source name:brain\|tissue:brain\|home tank:P1 lay1.1\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC WT rep9 [22 01879 S40]	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:WT\|Sex:male	GSM7813343	GSM7813343: Brain BC WT rep9 [22 01879 S40]; Danio rerio; RNA Seq	GSM7813343 r1	GSM7813343	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			22-01879_S40_R1_001.merged.fastq.gz 22-01879_S40_R2_001.merged.fastq.gz	fastq fastq	20379409680.0	103976580.0	GSM7813343 r1	0:98 1:98	A:5369707205;C:4764694596;G:4769087059;T:5472372608;N:3548212	98	98	5369707205	4764694596	4769087059	5472372608	3548212	SRX21926751	SRS19011081	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93829	0.93274	0.1147	0.11712	0.70485	0.70737	0.48791	0.48911	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
28427	28427	SRR26216323	SRX21926750	SRS19011080	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 rep8 [22 01877 S39]	GSM7813342	source name:brain\|tissue:brain\|home tank:P1 lay1.1\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC WT rep8 [22 01877 S39]	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:WT\|Sex:male	GSM7813342	GSM7813342: Brain BC WT rep8 [22 01877 S39]; Danio rerio; RNA Seq	GSM7813342 r1	GSM7813342	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			22-01877_S39_R1_001.merged.fastq.gz 22-01877_S39_R2_001.merged.fastq.gz	fastq fastq	20300298984.0	103572954.0	GSM7813342 r1	0:98 1:98	A:5322006867;C:4768036193;G:4786472382;T:5420285698;N:3497844	98	98	5322006867	4768036193	4786472382	5420285698	3497844	SRX21926750	SRS19011080	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93935	0.93555	0.10951	0.11139	0.70879	0.7094	0.48625	0.4844	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
28428	28428	SRR26216324	SRX21926749	SRS19011079	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 rep5 [22 01876 S38]	GSM7813341	source name:brain\|tissue:brain\|home tank:P2 lay3 tank1\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep5 [22 01876 S38]	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:P2 lay3 tank1\|genotype:MPSIIIB\|Sex:female	GSM7813341	GSM7813341: Brain BC MPSIIIB rep5 [22 01876 S38]; Danio rerio; RNA Seq	GSM7813341 r1	GSM7813341	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			22-01876_S38_R1_001.merged.fastq.gz 22-01876_S38_R2_001.merged.fastq.gz	fastq fastq	20658198904.0	105398974.0	GSM7813341 r1	0:98 1:98	A:5601204040;C:4656310461;G:4653067969;T:5744065008;N:3551426	98	98	5601204040	4656310461	4653067969	5744065008	3551426	SRX21926749	SRS19011079	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92156	0.92055	0.16792	0.17216	0.69739	0.6955	0.4896	0.49082	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
28429	28429	SRR26216325	SRX21926748	SRS19011078	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 rep7 [22 01875 S37]	GSM7813340	source name:brain\|tissue:brain\|home tank:P2 lay1 tank1\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep7 [22 01875 S37]	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:P2 lay1 tank1\|genotype:WT\|Sex:female	GSM7813340	GSM7813340: Brain BC WT rep7 [22 01875 S37]; Danio rerio; RNA Seq	GSM7813340 r1	GSM7813340	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			22-01875_S37_R1_001.merged.fastq.gz 22-01875_S37_R2_001.merged.fastq.gz	fastq fastq	19187850220.0	97897195.0	GSM7813340 r1	0:98 1:98	A:5098960652;C:4434084345;G:4444522551;T:5206970324;N:3312348	98	98	5098960652	4434084345	4444522551	5206970324	3312348	SRX21926748	SRS19011078	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93549	0.93041	0.12194	0.1247	0.70059	0.70145	0.49104	0.4936	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
28430	28430	SRR26216326	SRX21926747	SRS19011077	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 rep6 [22 01874 S36]	GSM7813339	source name:brain\|tissue:brain\|home tank:P2 lay3 tank1\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC WT rep6 [22 01874 S36]	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:P2 lay3 tank1\|genotype:WT\|Sex:male	GSM7813339	GSM7813339: Brain BC WT rep6 [22 01874 S36]; Danio rerio; RNA Seq	GSM7813339 r1	GSM7813339	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			22-01874_S36_R1_001.merged.fastq.gz 22-01874_S36_R2_001.merged.fastq.gz	fastq fastq	22842365672.0	116542682.0	GSM7813339 r1	0:98 1:98	A:6130106950;C:5210131371;G:5219905571;T:6278234629;N:3987151	98	98	6130106950	5210131371	5219905571	6278234629	3987151	SRX21926747	SRS19011077	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92799	0.92418	0.13514	0.13864	0.7035	0.70201	0.50044	0.50326	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
28431	28431	SRR26216327	SRX21926746	SRS19011076	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 MPSIIIC rep6 [22 01873 S35]	GSM7813338	source name:brain\|tissue:brain\|home tank:P2 lay3 tank1\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep6 [22 01873 S35]	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:P2 lay3 tank1\|genotype:MPSIIIC\|Sex:male	GSM7813338	GSM7813338: Brain BC MPSIIIC rep6 [22 01873 S35]; Danio rerio; RNA Seq	GSM7813338 r1	GSM7813338	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			22-01873_S35_R2_001.merged.fastq.gz 22-01873_S35_R1_001.merged.fastq.gz	fastq fastq	16529710176.0	84335256.0	GSM7813338 r1	0:98 1:98	A:4451252334;C:3754181517;G:3773431912;T:4547979245;N:2865168	98	98	4451252334	3754181517	3773431912	4547979245	2865168	SRX21926746	SRS19011076	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92964	0.92525	0.13434	0.13809	0.70698	0.70794	0.50154	0.49876	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
28432	28432	SRR26216328	SRX21926745	SRS19011075	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 MPSIIIC rep5 [22 01872 S34]	GSM7813337	source name:brain\|tissue:brain\|home tank:P2 lay1 tank2\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep5 [22 01872 S34]	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:P2 lay1 tank2\|genotype:MPSIIIC\|Sex:male	GSM7813337	GSM7813337: Brain BC MPSIIIC rep5 [22 01872 S34]; Danio rerio; RNA Seq	GSM7813337 r1	GSM7813337	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			22-01872_S34_R1_001.merged.fastq.gz 22-01872_S34_R2_001.merged.fastq.gz	fastq fastq	17967699064.0	91671934.0	GSM7813337 r1	0:98 1:98	A:4842209289;C:4058928742;G:4066249511;T:4997263523;N:3047999	98	98	4842209289	4058928742	4066249511	4997263523	3047999	SRX21926745	SRS19011075	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91823	0.9197	0.16266	0.16861	0.6999	0.69761	0.48703	0.48793	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
28433	28433	SRR26216329	SRX21926744	SRS19011074	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 MPSIIIC rep4 [22 01871 S33]	GSM7813336	source name:brain\|tissue:brain\|home tank:P2 lay1 tank1\|genotype:MPSIIIC\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep4 [22 01871 S33]	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:P2 lay1 tank1\|genotype:MPSIIIC\|Sex:female	GSM7813336	GSM7813336: Brain BC MPSIIIC rep4 [22 01871 S33]; Danio rerio; RNA Seq	GSM7813336 r1	GSM7813336	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			22-01871_S33_R2_001.merged.fastq.gz 22-01871_S33_R1_001.merged.fastq.gz	fastq fastq	17684828532.0	90228717.0	GSM7813336 r1	0:98 1:98	A:4726611575;C:4048652163;G:4054748200;T:4851839555;N:2977039	98	98	4726611575	4048652163	4054748200	4851839555	2977039	SRX21926744	SRS19011074	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92694	0.92539	0.1433	0.14788	0.70059	0.70039	0.48117	0.47985	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
28434	28434	SRR26216330	SRX21926743	SRS19011073	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 rep5 [22 01870 S32]	GSM7813335	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.1\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep5 [22 01870 S32]	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:P2 lay3 tank2.1\|genotype:WT\|Sex:female	GSM7813335	GSM7813335: Brain BC WT rep5 [22 01870 S32]; Danio rerio; RNA Seq	GSM7813335 r1	GSM7813335	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			22-01870_S32_R1_001.merged.fastq.gz 22-01870_S32_R2_001.merged.fastq.gz	fastq fastq	16763673808.0	85528948.0	GSM7813335 r1	0:98 1:98	A:4509188057;C:3795157983;G:3802083269;T:4654341788;N:2902711	98	98	4509188057	3795157983	3802083269	4654341788	2902711	SRX21926743	SRS19011073	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92254	0.92353	0.14925	0.15514	0.7025	0.70114	0.49102	0.48977	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
28435	28435	SRR26216331	SRX21926742	SRS19011072	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 rep4 [22 01869 S31]	GSM7813334	source name:brain\|tissue:brain\|home tank:P2 lay1 tank1\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep4 [22 01869 S31]	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:P2 lay1 tank1\|genotype:WT\|Sex:female	GSM7813334	GSM7813334: Brain BC WT rep4 [22 01869 S31]; Danio rerio; RNA Seq	GSM7813334 r1	GSM7813334	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			22-01869_S31_R2_001.merged.fastq.gz 22-01869_S31_R1_001.merged.fastq.gz	fastq fastq	16021352032.0	81741592.0	GSM7813334 r1										SRX21926742	SRS19011072	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92208	0.92219	0.15664	0.16229	0.70025	0.69879	0.49147	0.49026	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
28436	28436	SRR26216332	SRX21926741	SRS19011071	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 rep3 [22 01868 S30]	GSM7813333	source name:brain\|tissue:brain\|home tank:P2 lay1 tank2\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC WT rep3 [22 01868 S30]	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:P2 lay1 tank2\|genotype:WT\|Sex:male	GSM7813333	GSM7813333: Brain BC WT rep3 [22 01868 S30]; Danio rerio; RNA Seq	GSM7813333 r1	GSM7813333	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			22-01868_S30_R1_001.merged.fastq.gz 22-01868_S30_R2_001.merged.fastq.gz	fastq fastq	15332432220.0	78226695.0	GSM7813333 r1	0:98 1:98	A:4159395326;C:3427681764;G:3442087841;T:4300635995;N:2631294	98	98	4159395326	3427681764	3442087841	4300635995	2631294	SRX21926741	SRS19011071	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91474	0.91611	0.16784	0.1749	0.70573	0.70404	0.48815	0.48389	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
28437	28437	SRR26216333	SRX21926740	SRS19011070	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 rep2 [22 01867 S29]	GSM7813332	source name:brain\|tissue:brain\|home tank:P2 lay1 tank2\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC WT rep2 [22 01867 S29]	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:P2 lay1 tank2\|genotype:WT\|Sex:female	GSM7813332	GSM7813332: Brain BC WT rep2 [22 01867 S29]; Danio rerio; RNA Seq	GSM7813332 r1	GSM7813332	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			22-01867_S29_R1_001.merged.fastq.gz 22-01867_S29_R2_001.merged.fastq.gz	fastq fastq	14123797632.0	72060192.0	GSM7813332 r1	0:98 1:98	A:3794161474;C:3207083345;G:3218143109;T:3901992007;N:2417697	98	98	3794161474	3207083345	3218143109	3901992007	2417697	SRX21926740	SRS19011070	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92409	0.91991	0.15688	0.16104	0.70155	0.70027	0.49045	0.4913	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
28438	28438	SRR26216334	SRX21926739	SRS19011069	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 MPSIIIC rep3 [22 01866 S28]	GSM7813331	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.2\|genotype:MPSIIIC\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep3 [22 01866 S28]	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:P2 lay3 tank2.2\|genotype:MPSIIIC\|Sex:female	GSM7813331	GSM7813331: Brain BC MPSIIIC rep3 [22 01866 S28]; Danio rerio; RNA Seq	GSM7813331 r1	GSM7813331	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			22-01866_S28_R1_001.merged.fastq.gz 22-01866_S28_R2_001.merged.fastq.gz	fastq fastq	15245076196.0	77781001.0	GSM7813331 r1	0:98 1:98	A:4135875559;C:3414058363;G:3428678892;T:4263872270;N:2591112	98	98	4135875559	3414058363	3428678892	4263872270	2591112	SRX21926739	SRS19011069	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91726	0.91853	0.17756	0.18357	0.70494	0.70347	0.48952	0.49391	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
28439	28439	SRR26216335	SRX21926738	SRS19011068	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 MPSIIIC rep2 [22 01865 S27]	GSM7813330	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.2\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIC rep2 [22 01865 S27]	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:P2 lay3 tank2.2\|genotype:MPSIIIC\|Sex:male	GSM7813330	GSM7813330: Brain BC MPSIIIC rep2 [22 01865 S27]; Danio rerio; RNA Seq	GSM7813330 r1	GSM7813330	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			22-01865_S27_R1_001.merged.fastq.gz 22-01865_S27_R2_001.merged.fastq.gz	fastq fastq	15038751504.0	76728324.0	GSM7813330 r1	0:98 1:98	A:4106772665;C:3342615146;G:3356678074;T:4230068148;N:2617471	98	98	4106772665	3342615146	3356678074	4230068148	2617471	SRX21926738	SRS19011068	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91431	0.91483	0.17286	0.17947	0.70512	0.70508	0.49867	0.49437	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
28440	28440	SRR26216336	SRX21926737	SRS19011067	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 rep1 [22 01864 S26]	GSM7813329	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.2\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain BC WT rep1 [22 01864 S26]	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:P2 lay3 tank2.2\|genotype:WT\|Sex:male	GSM7813329	GSM7813329: Brain BC WT rep1 [22 01864 S26]; Danio rerio; RNA Seq	GSM7813329 r1	GSM7813329	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			22-01864_S26_R1_001.merged.fastq.gz 22-01864_S26_R2_001.merged.fastq.gz	fastq fastq	14585845288.0	74417578.0	GSM7813329 r1	0:98 1:98	A:4018411963;C:3192874484;G:3205170768;T:4166868705;N:2519368	98	98	4018411963	3192874484	3205170768	4166868705	2519368	SRX21926737	SRS19011067	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90578	0.90969	0.19878	0.20733	0.70656	0.70327	0.49101	0.49381	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
28441	28441	SRR26216337	SRX21926736	SRS19011066	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 rep4 [22 01863 S25]	GSM7813328	source name:brain\|tissue:brain\|home tank:P2 lay3 tank2.1\|genotype:MPSIIIB\|Sex:female\|geo loc name:missing\|collection date:missing	Brain BC MPSIIIB rep4 [22 01863 S25]	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:P2 lay3 tank2.1\|genotype:MPSIIIB\|Sex:female	GSM7813328	GSM7813328: Brain BC MPSIIIB rep4 [22 01863 S25]; Danio rerio; RNA Seq	GSM7813328 r1	GSM7813328	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			22-01863_S25_R1_001.merged.fastq.gz 22-01863_S25_R2_001.merged.fastq.gz	fastq fastq	12236162792.0	62429402.0	GSM7813328 r1	0:98 1:98	A:3402237481;C:2636320054;G:2656738248;T:3538765917;N:2101092	98	98	3402237481	2636320054	2656738248	3538765917	2101092	SRX21926736	SRS19011066	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.89964	0.9044	0.22191	0.23254	0.70871	0.70682	0.49884	0.49572	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
28442	28442	SRR26216338	SRX21926735	SRS19011065	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 AC MPSIIIA rep4 [22 01846 S8]	GSM7813311	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank6\|genotype:MPSIIIA\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep4 [22 01846 S8]	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:AC P2 lay1 tank6\|genotype:MPSIIIA\|Sex:male	GSM7813311	GSM7813311: Brain AC MPSIIIA rep4 [22 01846 S8]; Danio rerio; RNA Seq	GSM7813311 r1	GSM7813311	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			22-01846_S8_R1_001.merged.fastq.gz 22-01846_S8_R2_001.merged.fastq.gz	fastq fastq	16127355104.0	82282424.0	GSM7813311 r1	0:98 1:98	A:4403612584;C:3561549756;G:3579590782;T:4579822708;N:2779274	98	98	4403612584	3561549756	3579590782	4579822708	2779274	SRX21926735	SRS19011065	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91173	0.91641	0.18072	0.18991	0.70565	0.70378	0.48485	0.4827	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
28443	28443	SRR26216339	SRX21926734	SRS19011064	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 AC MPSIIIC rep2 [22 01845 S7]	GSM7813310	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank2\|genotype:MPSIIIC\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep2 [22 01845 S7]	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:AC P2 lay1 tank2\|genotype:MPSIIIC\|Sex:female	GSM7813310	GSM7813310: Brain AC MPSIIIC rep2 [22 01845 S7]; Danio rerio; RNA Seq	GSM7813310 r1	GSM7813310	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			22-01845_S7_R1_001.merged.fastq.gz 22-01845_S7_R2_001.merged.fastq.gz	fastq fastq	15508712072.0	79126082.0	GSM7813310 r1	0:98 1:98	A:4188137687;C:3513986940;G:3515000413;T:4288950665;N:2636367	98	98	4188137687	3513986940	3515000413	4288950665	2636367	SRX21926734	SRS19011064	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92402	0.9236	0.17078	0.17482	0.70226	0.70197	0.49018	0.48817	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
28444	28444	SRR26216340	SRX21926733	SRS19011063	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 AC WT rep2 [22 01844 S6]	GSM7813309	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank2\|genotype:WT\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC WT rep2 [22 01844 S6]	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:AC P2 lay1 tank2\|genotype:WT\|Sex:male	GSM7813309	GSM7813309: Brain AC WT rep2 [22 01844 S6]; Danio rerio; RNA Seq	GSM7813309 r1	GSM7813309	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			22-01844_S6_R1_001.merged.fastq.gz 22-01844_S6_R2_001.merged.fastq.gz	fastq fastq	16409825796.0	83723601.0	GSM7813309 r1	0:98 1:98	A:4471700709;C:3680179991;G:3683157895;T:4571927688;N:2859513	98	98	4471700709	3680179991	3683157895	4571927688	2859513	SRX21926733	SRS19011063	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.9212	0.92021	0.16733	0.17218	0.70782	0.70733	0.48416	0.48241	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
28445	28445	SRR26216341	SRX21926732	SRS19011062	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 AC MPSIIIA rep3 [22 01843 S5]	GSM7813308	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank2\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep3 [22 01843 S5]	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:AC P2 lay1 tank2\|genotype:MPSIIIA\|Sex:female	GSM7813308	GSM7813308: Brain AC MPSIIIA rep3 [22 01843 S5]; Danio rerio; RNA Seq	GSM7813308 r1	GSM7813308	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			22-01843_S5_R2_001.merged.fastq.gz 22-01843_S5_R1_001.merged.fastq.gz	fastq fastq	12529597920.0	63926520.0	GSM7813308 r1	0:98 1:98	A:3444508631;C:2752865530;G:2766555023;T:3563525948;N:2142788	98	98	3444508631	2752865530	2766555023	3563525948	2142788	SRX21926732	SRS19011062	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.90998	0.91217	0.19948	0.20656	0.70043	0.6985	0.49474	0.49331	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
28446	28446	SRR26216342	SRX21926731	SRS19011061	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 AC MPSIIIA rep2 [22 01842 S4]	GSM7813307	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank1\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep2 [22 01842 S4]	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:AC P2 lay1 tank1\|genotype:MPSIIIA\|Sex:female	GSM7813307	GSM7813307: Brain AC MPSIIIA rep2 [22 01842 S4]; Danio rerio; RNA Seq	GSM7813307 r1	GSM7813307	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			22-01842_S4_R1_001.merged.fastq.gz 22-01842_S4_R2_001.merged.fastq.gz	fastq fastq	16506577276.0	84217231.0	GSM7813307 r1	0:98 1:98	A:4457603132;C:3737370134;G:3742179917;T:4566576027;N:2848066	98	98	4457603132	3737370134	3742179917	4566576027	2848066	SRX21926731	SRS19011061	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.926	0.92349	0.16775	0.17157	0.70161	0.70134	0.49085	0.49135	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
28447	28447	SRR26216343	SRX21926730	SRS19011060	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 AC WT rep1 [22 01841 S3]	GSM7813306	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank1\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC WT rep1 [22 01841 S3]	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:AC P2 lay1 tank1\|genotype:WT\|Sex:female	GSM7813306	GSM7813306: Brain AC WT rep1 [22 01841 S3]; Danio rerio; RNA Seq	GSM7813306 r1	GSM7813306	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			22-01841_S3_R1_001.merged.fastq.gz 22-01841_S3_R2_001.merged.fastq.gz	fastq fastq	12185306672.0	62169932.0	GSM7813306 r1	0:98 1:98	A:3327952186;C:2717345655;G:2719684390;T:3418239630;N:2084811	98	98	3327952186	2717345655	2719684390	3418239630	2084811	SRX21926730	SRS19011060	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91958	0.91716	0.17632	0.18035	0.70264	0.70145	0.48946	0.49372	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
28448	28448	SRR26216344	SRX21926729	SRS19011059	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 AC MPSIIIC rep1 [22 01840 S2]	GSM7813305	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank1\|genotype:MPSIIIC\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIC rep1 [22 01840 S2]	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:AC P2 lay1 tank1\|genotype:MPSIIIC\|Sex:male	GSM7813305	GSM7813305: Brain AC MPSIIIC rep1 [22 01840 S2]; Danio rerio; RNA Seq	GSM7813305 r1	GSM7813305	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			22-01840_S2_R1_001.merged.fastq.gz 22-01840_S2_R2_001.merged.fastq.gz	fastq fastq	15366595608.0	78400998.0	GSM7813305 r1	0:98 1:98	A:4176085395;C:3454640713;G:3462167295;T:4271061985;N:2640220	98	98	4176085395	3454640713	3462167295	4271061985	2640220	SRX21926729	SRS19011059	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.9238	0.92066	0.16449	0.1677	0.70662	0.70577	0.49188	0.49263	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
28449	28449	SRR26216345	SRX21926728	SRS19011058	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 AC MPSIIIA rep1 [22 01839 S1]	GSM7813304	source name:brain\|tissue:brain\|home tank:AC P2 lay1 tank1\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AC MPSIIIA rep1 [22 01839 S1]	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:AC P2 lay1 tank1\|genotype:MPSIIIA\|Sex:female	GSM7813304	GSM7813304: Brain AC MPSIIIA rep1 [22 01839 S1]; Danio rerio; RNA Seq	GSM7813304 r1	GSM7813304	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			22-01839_S1_R1_001.merged.fastq.gz 22-01839_S1_R2_001.merged.fastq.gz	fastq fastq	12347212668.0	62995983.0	GSM7813304 r1	0:98 1:98	A:3347171972;C:2787017638;G:2791908611;T:3418993066;N:2121381	98	98	3347171972	2787017638	2791908611	3418993066	2121381	SRX21926728	SRS19011058	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92786	0.92297	0.15927	0.1621	0.70404	0.70431	0.49153	0.49029	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
28450	28450	SRR26216346	SRX21926727	SRS19011057	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 AB sgsh het rep2 [22 00152 S8]	GSM7813295	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:sgsh het\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AB sgsh het rep2 [22 00152 S8]	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:AB P1 lay1 tank2\|genotype:sgsh het\|Sex:male	GSM7813295	GSM7813295: Brain AB sgsh het rep2 [22 00152 S8]; Danio rerio; RNA Seq	GSM7813295 r1	GSM7813295	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			22-00152_S8_R2_001.merged.fastq.gz 22-00152_S8_R1_001.merged.fastq.gz	fastq fastq	25966816372.0	132483757.0	GSM7813295 r1	0:98 1:98	A:6973183255;C:5877834155;G:5930243960;T:7177178083;N:8376919	98	98	6973183255	5877834155	5930243960	7177178083	8376919	SRX21926727	SRS19011057	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92369	0.92575	0.15407	0.16762	0.70224	0.70244	0.49045	0.48532	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
28451	28451	SRR26216347	SRX21926726	SRS19011056	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 AB WT rep3 [22 00151 S7]	GSM7813294	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB WT rep3 [22 00151 S7]	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:AB P1 lay1 tank2\|genotype:WT\|Sex:female	GSM7813294	GSM7813294: Brain AB WT rep3 [22 00151 S7]; Danio rerio; RNA Seq	GSM7813294 r1	GSM7813294	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			22-00151_S7_R1_001.merged.fastq.gz 22-00151_S7_R2_001.merged.fastq.gz	fastq fastq	20429512180.0	104232205.0	GSM7813294 r1	0:98 1:98	A:5524943642;C:4569903416;G:4618023597;T:5709981807;N:6659718	98	98	5524943642	4569903416	4618023597	5709981807	6659718	SRX21926726	SRS19011056	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91753	0.92093	0.17609	0.1946	0.70705	0.70498	0.49526	0.49595	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
28452	28452	SRR26216348	SRX21926725	SRS19011055	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 AB WT rep2 [22 00150 S6]	GSM7813293	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB WT rep2 [22 00150 S6]	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:AB P1 lay1 tank2\|genotype:WT\|Sex:female	GSM7813293	GSM7813293: Brain AB WT rep2 [22 00150 S6]; Danio rerio; RNA Seq	GSM7813293 r1	GSM7813293	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			22-00150_S6_R1_001.merged.fastq.gz 22-00150_S6_R2_001.merged.fastq.gz	fastq fastq	20872419064.0	106491934.0	GSM7813293 r1	0:98 1:98	A:5631355778;C:4682808382;G:4724172615;T:5827274589;N:6807700	98	98	5631355778	4682808382	4724172615	5827274589	6807700	SRX21926725	SRS19011055	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91815	0.9219	0.1737	0.19345	0.70329	0.70299	0.4931	0.48343	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
28453	28453	SRR26216349	SRX21926724	SRS19011054	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 AB sgsh het rep1 [22 00148 S5]	GSM7813292	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:sgsh het\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB sgsh het rep1 [22 00148 S5]	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:AB P1 lay1 tank2\|genotype:sgsh het\|Sex:female	GSM7813292	GSM7813292: Brain AB sgsh het rep1 [22 00148 S5]; Danio rerio; RNA Seq	GSM7813292 r1	GSM7813292	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			22-00148_S5_R2_001.merged.fastq.gz 22-00148_S5_R1_001.merged.fastq.gz	fastq fastq	22105679288.0	112784078.0	GSM7813292 r1	0:98 1:98	A:5823448386;C:5145130246;G:5179195236;T:5950683795;N:7221625	98	98	5823448386	5145130246	5179195236	5950683795	7221625	SRX21926724	SRS19011054	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.93457	0.93377	0.12761	0.13206	0.70569	0.70867	0.48476	0.48428	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
28454	28454	SRR26216350	SRX21926723	SRS19011053	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 AB MPSIIIA rep2 [22 00147 S4]	GSM7813291	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:MPSIIIA\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIA rep2 [22 00147 S4]	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:AB P1 lay1 tank2\|genotype:MPSIIIA\|Sex:male	GSM7813291	GSM7813291: Brain AB MPSIIIA rep2 [22 00147 S4]; Danio rerio; RNA Seq	GSM7813291 r1	GSM7813291	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			22-00147_S4_R1_001.merged.fastq.gz 22-00147_S4_R2_001.merged.fastq.gz	fastq fastq	24994383540.0	127522365.0	GSM7813291 r1	0:98 1:98	A:6713459564;C:5636288152;G:5694678404;T:6941948817;N:8008603	98	98	6713459564	5636288152	5694678404	6941948817	8008603	SRX21926723	SRS19011053	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91898	0.92159	0.17146	0.18718	0.70201	0.70161	0.48479	0.48311	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
28455	28455	SRR26216351	SRX21926722	SRS19011052	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 AB WT rep1 [22 00145 S3]	GSM7813290	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank4\|genotype:WT\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB WT rep1 [22 00145 S3]	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:AB P1 lay1 tank4\|genotype:WT\|Sex:female	GSM7813290	GSM7813290: Brain AB WT rep1 [22 00145 S3]; Danio rerio; RNA Seq	GSM7813290 r1	GSM7813290	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			22-00145_S3_R1_001.merged.fastq.gz 22-00145_S3_R2_001.merged.fastq.gz	fastq fastq	21971383420.0	112098895.0	GSM7813290 r1	0:98 1:98	A:5817485267;C:5059820956;G:5101690277;T:5985434835;N:6952085	98	98	5817485267	5059820956	5101690277	5985434835	6952085	SRX21926722	SRS19011052	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.92434	0.9301	0.13339	0.14984	0.70181	0.70013	0.48702	0.48827	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
28456	28456	SRR26216352	SRX21926721	SRS19011051	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 AB MPSIIIA rep1 [22 00138 S2]	GSM7813289	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIA rep1 [22 00138 S2]	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:AB P1 lay1 tank3\|genotype:MPSIIIA\|Sex:female	GSM7813289	GSM7813289: Brain AB MPSIIIA rep1 [22 00138 S2]; Danio rerio; RNA Seq	GSM7813289 r1	GSM7813289	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			22-00138_S2_R1_001.merged.fastq.gz 22-00138_S2_R2_001.merged.fastq.gz	fastq fastq	20393895648.0	104050488.0	GSM7813289 r1	0:98 1:98	A:5535222513;C:4521860121;G:4564229476;T:5765827363;N:6756175	98	98	5535222513	4521860121	4564229476	5765827363	6756175	SRX21926721	SRS19011051	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.91058	0.91708	0.19504	0.22041	0.69741	0.69392	0.4866	0.4891	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
28457	28457	SRR26216353	SRX21926720	SRS19011050	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 AB MPSIIIB rep1 [22 00136 S1]	GSM7813288	source name:brain\|tissue:brain\|home tank:AB P1 lay1 tank2\|genotype:MPSIIIB\|Sex:male\|geo loc name:missing\|collection date:missing	Brain AB MPSIIIB rep1 [22 00136 S1]	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:AB P1 lay1 tank2\|genotype:MPSIIIB\|Sex:male	GSM7813288	GSM7813288: Brain AB MPSIIIB rep1 [22 00136 S1]; Danio rerio; RNA Seq	GSM7813288 r1	GSM7813288	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			22-00136_S1_R1_001.merged.fastq.gz 22-00136_S1_R2_001.merged.fastq.gz	fastq fastq	22736679532.0	116003467.0	GSM7813288 r1	0:98 1:98	A:6160987473;C:5083325909;G:5143258939;T:6341622029;N:7485182	98	98	6160987473	5083325909	5143258939	6341622029	7485182	SRX21926720	SRS19011050	SRA1723608	The University of Adelaide	The University of Adelaide	2	0.918	0.92042	0.18082	0.19533	0.70301	0.70195	0.49	0.48891	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
29191	29191	SRR27308233	SRX22985581	SRS19950789	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP /sp7+ Osteoblast rep2	GSM7987448	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Osteoblasts\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP /sp7+ Osteoblast rep2	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Osteoblasts\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987448	GSM7987448: EGFP /sp7+ Osteoblast rep2; Danio rerio; RNA Seq	GSM7987448 r1	GSM7987448	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Ob-GR2_S6_R2_001.fastq.gz Ob-GR2_S6_R1_001.fastq.gz	fastq fastq	6044999600.0	15112499.0	GSM7987448 r1	0:200 1:200	A:1547731745;C:1388120378;G:1581574912;T:1523597213;N:3975352	200	200	1547731745	1388120378	1581574912	1523597213	3975352	SRX22985581	SRS19950789	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.36888	0.02272	0.01109	0.00038	0.86914	0.99328	0.46943	0.4982	200	200	B	T	mate2 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
29192	29192	SRR27308234	SRX22985580	SRS19950790	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP /sp7+ Osteoblast rep1	GSM7987447	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Osteoblasts\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP /sp7+ Osteoblast rep1	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Osteoblasts\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987447	GSM7987447: EGFP /sp7+ Osteoblast rep1; Danio rerio; RNA Seq	GSM7987447 r1	GSM7987447	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Ob-GR_S77_R1_001.fastq.gz Ob-GR_S77_R2_001.fastq.gz	fastq fastq	4847773600.0	12119434.0	GSM7987447 r1	0:200 1:200	A:1242312480;C:1120397684;G:1256425065;T:1226991694;N:1646677	200	200	1242312480	1120397684	1256425065	1226991694	1646677	SRX22985580	SRS19950790	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.0146	0.02559	0.00038	0.00052	0.99397	0.99405	0.50471	0.47146	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
29193	29193	SRR27308235	SRX22985579	SRS19950788	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP+/sp7+ OMP rep2	GSM7987446	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Osteogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP+/sp7+ OMP rep2	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Osteogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987446	GSM7987446: EGFP+/sp7+ OMP rep2; Danio rerio; RNA Seq	GSM7987446 r1	GSM7987446	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Ob-G2_S5_R2_001.fastq.gz Ob-G2_S5_R1_001.fastq.gz	fastq fastq	6253558800.0	15633897.0	GSM7987446 r1	0:200 1:200	A:1638931864;C:1404420075;G:1600115132;T:1605939571;N:4152158	200	200	1638931864	1404420075	1600115132	1605939571	4152158	SRX22985579	SRS19950788	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.41021	0.02334	0.01523	0.00074	0.83989	0.99099	0.52255	0.52173	200	200	B	T	mate2 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
29194	29194	SRR27308236	SRX22985578	SRS19950791	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP+/sp7+ OMP rep1	GSM7987445	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Osteogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP+/sp7+ OMP rep1	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Osteogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987445	GSM7987445: EGFP+/sp7+ OMP rep1; Danio rerio; RNA Seq	GSM7987445 r1	GSM7987445	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Ob-G_S28_R2_001.fastq.gz Ob-G_S28_R1_001.fastq.gz	fastq fastq	4832320400.0	12080801.0	GSM7987445 r1	0:200 1:200	A:1252095509;C:1107971153;G:1236349772;T:1233319775;N:2584191	200	200	1252095509	1107971153	1236349772	1233319775	2584191	SRX22985578	SRS19950791	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.01133	0.02895	0.00033	0.00043	0.99439	0.99297	0.50298	0.45574	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
29195	29195	SRR27308237	SRX22985577	SRS19950787	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP+/sp7 CMP rep2	GSM7987444	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Chondrogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP+/sp7 CMP rep2	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Chondrogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987444	GSM7987444: EGFP+/sp7 CMP rep2; Danio rerio; RNA Seq	GSM7987444 r1	GSM7987444	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Mes-G2_S4_R1_001.fastq.gz Mes-G2_S4_R2_001.fastq.gz	fastq fastq	5812163600.0	14530409.0	GSM7987444 r1	0:200 1:200	A:1538664561;C:1291748975;G:1473028809;T:1504905134;N:3816121	200	200	1538664561	1291748975	1473028809	1504905134	3816121	SRX22985577	SRS19950787	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.40138	0.02482	0.0176	0.00091	0.83918	0.99099	0.47875	0.43124	200	200	B	T	mate2 technical by mapping diff	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
29196	29196	SRR27308238	SRX22985576	SRS19950786	SRP479308	PRJNA1055256	Independent mesenchymal progenitor pools respectively produce and maintain osteogenic and chondrogenic cells in zebrafish	GSE251757	Transcriptome Analysis	Skeletal tissues including cartilage and bones are characteristic features of vertebrates that are crucial for supporting body morphology and locomotion. Studies mainly in mice have shown that osteoblasts and chondroblasts are supplied from several progenitors in development growth and homeostasis. However developmental origins of osteoblasts and chondroblasts lineage relationship progenitor cells and their differentiation potentials throughout animal life are not seamlessly understood. In this study we used clonal cell tracking in zebrafish and found that sox9a+ cells are committed to either chondrogenic or osteogenic fates during embryonic stages and that respective progenies are independently maintained as mesenchymal progenitor pools. Once committed they never change their lineage identities throughout their lives even through regeneration. We further showed that osteogenic mesenchymal cells replenish the osteoblast progenitor cells OPCs which are the reserved stem cells for osteoblast production during regeneration and homeostasis. Independent mesenchymal progenitors dedicated to produce either chondroblasts or osteoblasts would be important targets for skeletal tissue regeneration. Overall design: To investigate the lineage relationship between mesenchymal cells and osteoblasts in the zebrafish caudal fin we isolated sp7 mesenchymal cells and sp7+ osteoblasts derived from sox9a+ somite cells from 14 dy post amputation dpa caudal fin by fluorescence activated cell sorting. We then performed gene expression profiling analysis using data obtained from RNA seq of 3 different cells. Comparative gene expression profiling analysis of RNA seq data for osteogenic mesenchymal progenitors OMPs chondrogenic mesenchymal progenitors CMPs and osteoblasts.	pubmed:38193362		EGFP+/sp7 CMP rep1	GSM7987443	source name:14 dpa adult caudal fin\|tissue:14 dpa adult caudal fin\|cell type:Chondrogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry\|geo loc name:missing\|collection date:missing	EGFP+/sp7 CMP rep1	High quality reads were mapped using hisat2 ver. 2.2.1. Trimmed sequence reads were mapped to GRCz11 using hisat2. Read count extraction and normalization were performed using featureCounts ver. 2.0.3. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes basic gene information gene id length Genbank id RNA type gene name product raw count RPKM and TPM values.	14 dpa adult caudal fin	Different types of cells were sorted by the fluorescence activated cell sorter SH800S SONY.	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.	Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild type zebrafish Danio rerio strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.	tissue:14 dpa adult caudal fin\|cell type:Chondrogenic mesenchymal progenitors\|genotype:Tgcryaa:EGFP sox9a:Cre ERt2; Ola.Actb:loxp TagBFP loxp EGFP; Ola.Sp7:mCherry	GSM7987443	GSM7987443: EGFP+/sp7 CMP rep1; Danio rerio; RNA Seq	GSM7987443 r1	GSM7987443	1	The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit Qiagen. RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer's protocol.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP479308			Mes-G_S15_R1_001.fastq.gz Mes-G_S15_R2_001.fastq.gz	fastq fastq	5321588000.0	13303970.0	GSM7987443 r1	0:200 1:200	A:1405233304;C:1195662643;G:1342003810;T:1376732727;N:1955516	200	200	1405233304	1195662643	1342003810	1376732727	1955516	SRX22985576	SRS19950786	SRA1773396	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	Kawakami lab, School of Life Science and Technology, Tokyo Institute of Technology	2	0.00961	0.02419	0.00032	0.00052	0.9945	0.99324	0.51073	0.48429	200	200	T	T	mates < 9% mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Japan	2023-12-20	Adult	Adult	Fin	Surface Structure
31980	31980	SRR28892728	SRX24451189	SRS21204958	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				TP3	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 6\|BioSampleModel:Model organism or animal									Adult zebrafish liver	TP3	TP3	mRNAseq of zebrafish liver replication 3 of TP		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			TP3_1.fq.gz TP3_2.fq.gz	fastq fastq	6657069900.0	22190233.0	TP3 1.fq.gz	0:150 1:150	A:1808410149;C:1512668682;G:1536153888;T:1799837181;N:0	150	150	1808410149	1512668682	1536153888	1799837181	0	SRX24451189	SRS21204958	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
31981	31981	SRR28892729	SRX24451188	SRS21204959	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				TP2	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 5\|BioSampleModel:Model organism or animal									Adult zebrafish liver	TP2	TP2	mRNAseq of zebrafish liver replication 2 of TP		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			TP2_1.fq.gz TP2_2.fq.gz	fastq fastq	6617368500.0	22057895.0	TP2 1.fq.gz	0:150 1:150	A:1799646726;C:1503407966;G:1523443584;T:1790870224;N:0	150	150	1799646726	1503407966	1523443584	1790870224	0	SRX24451188	SRS21204959	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
31982	31982	SRR28892730	SRX24451187	SRS21204956	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				TP1	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 4\|BioSampleModel:Model organism or animal									Adult zebrafish liver	TP1	TP1	mRNAseq of zebrafish liver replication 1 of TP		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			TP1_1.fq.gz TP1_2.fq.gz	fastq fastq	6432586800.0	21441956.0	TP1 1.fq.gz	0:150 1:150	A:1743341515;C:1465440262;G:1488109144;T:1735695879;N:0	150	150	1743341515	1465440262	1488109144	1735695879	0	SRX24451187	SRS21204956	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
31983	31983	SRR28892731	SRX24451186	SRS21204957	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				CONT3	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 3\|BioSampleModel:Model organism or animal									Adult zebrafish liver	CON3	CON3	mRNAseq of zebrafish liver replication 3 of CONT		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			CONT3_1.fq.gz CONT3_2.fq.gz	fastq fastq	6595768200.0	21985894.0	CONT3 1.fq.gz	0:150 1:150	A:1762107185;C:1525175684;G:1547321856;T:1761163475;N:0	150	150	1762107185	1525175684	1547321856	1761163475	0	SRX24451186	SRS21204957	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
31984	31984	SRR28892732	SRX24451185	SRS21204954	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				CONT2	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 2\|BioSampleModel:Model organism or animal									Adult zebrafish liver	CON2	CON2	mRNAseq of zebrafish liver replication 2 of CONT		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			CONT2_1.fq.gz CONT2_2.fq.gz	fastq fastq	6175346400.0	20584488.0	CONT2 1.fq.gz	0:150 1:150	A:1656546719;C:1421990443;G:1442409824;T:1654399414;N:0	150	150	1656546719	1421990443	1442409824	1654399414	0	SRX24451185	SRS21204954	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
31985	31985	SRR28892733	SRX24451184	SRS21204955	SRP505641	PRJNA1107713	Tea polyphenols induce hepatotoxicity by interfering with adult zebrafish lipid metabolism and gut microbiota through the gut liver axis	PRJNA1107713	Other	High dose tea polyphenols may promote fatty acid absorption by hepatocytes by up regulating FABP CD36 and SRB1 genes inhibiting fatty acid efflux by down regulating ABCA1 genes and inhibiting fatty acid beta oxidation by down regulating CPT1 and ACAA2 genes resulting in fat accumulation in hepatocytes upregulation of inflammatory pathways and increased expression of pro inflammatory factors TNF a and IL1 b.				CONT1	strain:not applicable\|isolate:not applicable\|breed:not collected\|cultivar:not applicable\|ecotype:AB ecotype\|age:5 month\|collection date:2022 11 24\|geo loc name:China\|sex:male\|tissue:liver\|replicate:replicate=biological replicate 1\|BioSampleModel:Model organism or animal									Adult zebrafish liver	CON1	CON1	mRNAseq of zebrafish liver replication 1 of CONT		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP505641			CONT1_1.fq.gz CONT1_2.fq.gz	fastq fastq	6342828300.0	21142761.0	CONT1 1.fq.gz	0:150 1:150	A:1698306803;C:1464261565;G:1482929449;T:1697330483;N:0	150	150	1698306803	1464261565	1482929449	1697330483	0	SRX24451184	SRS21204955	SRA1858747	Beibu Gulf University\|college of Food Engineering	Beibu Gulf University												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2024-05-04	Adult	Adult	Liver	Liver and Biliary System
34508	34508	SRR32041235	SRX27390499	SRS23823272	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 3 group	Cr+VC 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300476	EHK0300476	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz	fastq fastq	6579236402.0	21785551.0	Cr+VC 3.R1.raw.fastq.gz	0:151 1:151	A:1950296368;C:1342383640;G:1373591474;T:1912893257;N:71663	151	151	1950296368	1342383640	1373591474	1912893257	71663	SRX27390499	SRS23823272	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34509	34509	SRR32041236	SRX27390498	SRS23823271	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 2 group	Cr+VC 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300475	EHK0300475	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz	fastq fastq	7431192898.0	24606599.0	Cr+VC 2.R1.raw.fastq.gz	0:151 1:151	A:2185434880;C:1533450452;G:1567401090;T:2144825061;N:81415	151	151	2185434880	1533450452	1567401090	2144825061	81415	SRX27390498	SRS23823271	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34510	34510	SRR32041237	SRX27390497	SRS23823270	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI]+VC 1 group	Cr+VC 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 14\|health state:health\|sample type:tissue\|lep:Cr+VC 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300474	EHK0300474	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr+VC-1.R1.raw.fastq.gz Cr+VC-1.R2.raw.fastq.gz	fastq fastq	6385666180.0	21144590.0	Cr+VC 1.R1.raw.fastq.gz	0:151 1:151	A:1864936934;C:1329491594;G:1363211111;T:1827956599;N:69942	151	151	1864936934	1329491594	1363211111	1827956599	69942	SRX27390497	SRS23823270	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34511	34511	SRR32041238	SRX27390496	SRS23823269	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 3 group	Cr 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300473	EHK0300473	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz	fastq fastq	6339933716.0	20993158.0	Cr 3.R1.raw.fastq.gz	0:151 1:151	A:1873178321;C:1296125569;G:1333622723;T:1836939106;N:67997	151	151	1873178321	1296125569	1333622723	1836939106	67997	SRX27390496	SRS23823269	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34512	34512	SRR32041239	SRX27390495	SRS23823268	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 2 group	Cr 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300472	EHK0300472	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr-2.R1.raw.fastq.gz Cr-2.R2.raw.fastq.gz	fastq fastq	6461518010.0	21395755.0	Cr 2.R1.raw.fastq.gz	0:151 1:151	A:1878799067;C:1352321588;G:1386809443;T:1843520259;N:67653	151	151	1878799067	1352321588	1386809443	1843520259	67653	SRX27390495	SRS23823268	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34513	34513	SRR32041240	SRX27390494	SRS23823267	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr[VI] 1 group	Cr 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 13\|health state:health\|sample type:tissue\|lep:Cr 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300471	EHK0300471	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz	fastq fastq	7143701582.0	23654641.0	Cr 1.R1.raw.fastq.gz	0:151 1:151	A:1955056767;C:1615392059;G:1650478323;T:1922695182;N:79251	151	151	1955056767	1615392059	1650478323	1922695182	79251	SRX27390494	SRS23823267	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34514	34514	SRR32041241	SRX27390493	SRS23823266	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 3 group	Con 3	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300470	EHK0300470	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz	fastq fastq	6474159730.0	21437615.0	Con 3.R1.raw.fastq.gz	0:151 1:151	A:1937289968;C:1298659806;G:1337603954;T:1900535989;N:70013	151	151	1937289968	1298659806	1337603954	1900535989	70013	SRX27390493	SRS23823266	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34515	34515	SRR32041242	SRX27390492	SRS23823265	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 2 group	Con 2	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300469	EHK0300469	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz	fastq fastq	8372440828.0	27723314.0	Con 2.R1.raw.fastq.gz	0:151 1:151	A:2235968446;C:1933538809;G:1977416201;T:2225425413;N:91959	151	151	2235968446	1933538809	1977416201	2225425413	91959	SRX27390492	SRS23823265	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34516	34516	SRR32041243	SRX27390491	SRS23823264	SRP558202	PRJNA1212333	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212333	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			control 1 group	Con 1	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:brain\|death date:2023 8 12\|health state:health\|sample type:tissue\|lep:Con 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	EHK0300468	EHK0300468	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558202			Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz	fastq fastq	6527063486.0	21612793.0	Con 1.R1.raw.fastq.gz	0:151 1:151	A:1939230604;C:1326702799;G:1357063348;T:1903995450;N:71285	151	151	1939230604	1326702799	1357063348	1903995450	71285	SRX27390491	SRS23823264	SRA2054545	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-18	Adult	Adult	Brain	Nervous System
34517	34517	SRR32044795	SRX27393953	SRS23824014	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr+VC 3	I	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 3	Cr+VC 3	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz	fastq fastq	6773536558.0	22428929.0	Cr+VC 3.R1.raw.fastq.gz	0:151 1:151	A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278	151	151	1792253952	1581454013	1629330621	1770470694	27278	SRX27393953	SRS23824014	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34518	34518	SRR32044796	SRX27393952	SRS23824013	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr+VC 2	H	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 2	Cr+VC 2	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz	fastq fastq	7449518862.0	24667281.0	Cr+VC 2.R1.raw.fastq.gz	0:151 1:151	A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119	151	151	1969693675	1748150730	1771267240	1960378098	29119	SRX27393952	SRS23824013	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34519	34519	SRR32044797	SRX27393951	SRS23824012	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr+VC 1	G	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 14\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 14\|health state:health\|sample type:tissue\|replication:Cr+VC 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr+VC 1	Cr+VC 1	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295		loader:fastq load.py\|options: doNotUseSharq	Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq	fastq fastq	6865491179.0	45466829.0	Cr+VC 1.R1.raw.fastq.gz	0:151	A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474	151		1830069736	1600281531	1626303427	1808809011	27474	SRX27393951	SRS23824012	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34520	34520	SRR32044798	SRX27393950	SRS23824011	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr 3	F	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 3	Cr 3	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz	fastq fastq	6069804078.0	20098689.0	Cr 3.R1.raw.fastq.gz	0:151 1:151	A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079	151	151	1603886661	1431213970	1440806224	1593873144	24079	SRX27393950	SRS23824011	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34521	34521	SRR32044799	SRX27393949	SRS23824010	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr 2	E	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 2	Cr 2	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295		loader:fastq load.py\|options: doNotUseSharq	Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq	fastq fastq	8327156985.0	55146735.0	Cr 2.R1.raw.fastq.gz	0:151	A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145	151		2181317777	1974793526	2003240106	2167771431	34145	SRX27393949	SRS23824010	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34522	34522	SRR32044800	SRX27393948	SRS23824009	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Cr 1	D	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 13\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 13\|health state:health\|sample type:tissue\|replication:Cr 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Cr 1	Cr 1	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz	fastq fastq	7322067614.0	24245257.0	Cr 1.R1.raw.fastq.gz	0:151 1:151	A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557	151	151	1927213281	1727973559	1748866497	1917985720	28557	SRX27393948	SRS23824009	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34523	34523	SRR32044801	SRX27393947	SRS23824008	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Con 3	C	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 3\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 3	Con 3	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz	fastq fastq	10329187314.0	34202607.0	Con 3.R1.raw.fastq.gz	0:151 1:151	A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354	151	151	2805764955	2343400161	2421657823	2758323021	41354	SRX27393947	SRS23824008	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34524	34524	SRR32044802	SRX27393946	SRS23824007	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Con 2	B	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 2\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 2	Con 2	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz	fastq fastq	10789961398.0	35728349.0	Con 2.R1.raw.fastq.gz	0:151 1:151	A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353	151	151	2983305704	2396592872	2488165589	2921853880	43353	SRX27393946	SRS23824007	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34525	34525	SRR32044803	SRX27393945	SRS23824006	SRP558295	PRJNA1212482	vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish	PRJNA1212482	Other	Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.			Con 1	A	ecotype:wild type zebrafish\|age:6 month\|dev stage:adult\|collection date:2023 08 12\|geo loc name:China: Haikou Hainan Province\|sex:pooled male and female\|tissue:gut\|death date:2023 8 12\|health state:health\|sample type:tissue\|replication:Con 1\|BioSampleModel:Model organism or animal									RNA Seq of brian:Adult female and male zebrafish	Con 1	Con 1	normal		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-T7	SRP558295			Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz	fastq fastq	7118179260.0	23570130.0	Con 1.R1.raw.fastq.gz	0:151 1:151	A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275	151	151	1874284939	1673861890	1718740497	1851263659	28275	SRX27393945	SRS23824006	SRA2054568	Hainan University\|School of Life and Health Sciences	Hainan University												B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	China	2025-01-19	Adult	Adult	Gut	Digestive System
34877	34877	SRR32303701	SRX27639471	SRS24046086	SRP563065	PRJNA1221811	Targeted selection of experimental replicate groups is the likely driver of differential expression artifacts	GSE289151	Transcriptome Analysis	The design of a scientific experiment forms the foundation for rigorous hypothesis testing and robust interpretations. In RNA seq analyses where common model organisms are used to study the effects of gene perturbations breeding schemes are typically designed to produce siblings with either mutant or wildtype alleles of a gene. Siblings are expected to possess reduced genetic variability allowing the biological responses of a gene perturbation to be observed accurately and above that of minimal background noise. However as previously reported Baer et al. 2024 inter and intra genetic variability of the parental subjects allows for the possibility of such between the progeny. What matters is not so much the genetic diversity but more specifically the differences in polymorphic loci represented between replicate sample groups which are constructed to perform comparative statistical tests. This is largely due to chance when selecting a subset of progeny at random to ultimately represent the RNA sequencing samples. For many RNA sequencing experiments this subset is often small due to minimise costs and therefore the opportunity of skewing is likely. Additionally when the subset of samples is not selected at random particularly when defined based on genotype at a genetic locus further skewing may artificially and unexpectedly be introduced. The end result is expression differences due to unequal representations of genetic features that influence gene expression i.e. expression quantitative trai loci eQTLs which manifest as noise obscuring the desired signal and therefore confound interpretations. In this study we intentionally implemented an experimental design that opposes our advice from previous findings. We analyse the impacts of strain specific differences in zebrafish by outcrossing two different strains of zebrafish. Strain specific differences were quantified by performing Differential Allelic Representation DAR analysis consequently providing additional evidence that DAR contributes to false po…			Whole brain chr17 T428del/+ chr14 TU/PK rep3	GSM8785378	source name:Whole brain\|tissue:Whole brain\|genotype:chr17 T428del/+; chr14 TU/PK\|batch:1\|geo loc name:missing\|collection date:missing	Whole brain chr17 T428del/+ chr14 TU/PK rep3	Raw reads were trimmed with fastp v0.23.4 with parameters: detect adapter for pe qualified quality phred 20 length required 35 trim poly g Trimmed reads were aligned to GRCz11 Ensembl release 111 with STAR v2.7.11b with parameters: sjdbOverhang 149 outSAMtype BAM SortedByCoordinate twopassMode Basic Aligned reads were summarised to the gene level using Subread featureCounts v2.0.6 with parameters: p countReadPairs fracOverlap 1 minOverlap 35 Assembly: GRCz11 Supplementary files format and content: Processed data contains gene level counts as output by featureCounts in TSV format.	Whole brain		RNA was extracted from whole brain tissue using Qiagen RNeasy columns. Stranded polyA libraries prepared according to the Nugen Universal Plus mRNA seq protocol and included 13 cycles of amplification.		tissue:Whole brain\|genotype:chr17 T428del/+; chr14 TU/PK\|batch:1	GSM8785378	GSM8785378: Whole brain chr17 T428del/+ chr14 TU/PK rep3; Danio rerio; RNA Seq	GSM8785378 r1	GSM8785378	1	RNA was extracted from whole brain tissue using Qiagen RNeasy columns. Stranded polyA libraries prepared according to the Nugen Universal Plus mRNA seq protocol and included 13 cycles of amplification.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP563065			SAGCFN_23_00423_S27_R1_001.fastq.gz SAGCFN_23_00423_S27_R2_001.fastq.gz	fastq fastq	21983734400.0	109918672.0	GSM8785378 r1	0:100 1:100	A:6067597899;C:4889387435;G:4903291823;T:6123135261;N:321982	100	100	6067597899	4889387435	4903291823	6123135261	321982	SRX27639471	SRS24046086	SRA2076182	The University of Adelaide	The University of Adelaide												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2025-02-10	Undetermined	Adult	Brain	Nervous System
34878	34878	SRR32303702	SRX27639470	SRS24046085	SRP563065	PRJNA1221811	Targeted selection of experimental replicate groups is the likely driver of differential expression artifacts	GSE289151	Transcriptome Analysis	The design of a scientific experiment forms the foundation for rigorous hypothesis testing and robust interpretations. In RNA seq analyses where common model organisms are used to study the effects of gene perturbations breeding schemes are typically designed to produce siblings with either mutant or wildtype alleles of a gene. Siblings are expected to possess reduced genetic variability allowing the biological responses of a gene perturbation to be observed accurately and above that of minimal background noise. However as previously reported Baer et al. 2024 inter and intra genetic variability of the parental subjects allows for the possibility of such between the progeny. What matters is not so much the genetic diversity but more specifically the differences in polymorphic loci represented between replicate sample groups which are constructed to perform comparative statistical tests. This is largely due to chance when selecting a subset of progeny at random to ultimately represent the RNA sequencing samples. For many RNA sequencing experiments this subset is often small due to minimise costs and therefore the opportunity of skewing is likely. Additionally when the subset of samples is not selected at random particularly when defined based on genotype at a genetic locus further skewing may artificially and unexpectedly be introduced. The end result is expression differences due to unequal representations of genetic features that influence gene expression i.e. expression quantitative trai loci eQTLs which manifest as noise obscuring the desired signal and therefore confound interpretations. In this study we intentionally implemented an experimental design that opposes our advice from previous findings. We analyse the impacts of strain specific differences in zebrafish by outcrossing two different strains of zebrafish. Strain specific differences were quantified by performing Differential Allelic Representation DAR analysis consequently providing additional evidence that DAR contributes to false po…			Whole brain chr17 W233fs/+ chr14 PK/PK rep3	GSM8785377	source name:Whole brain\|tissue:Whole brain\|genotype:chr17 W233fs/+; chr14 PK/PK\|batch:1\|geo loc name:missing\|collection date:missing	Whole brain chr17 W233fs/+ chr14 PK/PK rep3	Raw reads were trimmed with fastp v0.23.4 with parameters: detect adapter for pe qualified quality phred 20 length required 35 trim poly g Trimmed reads were aligned to GRCz11 Ensembl release 111 with STAR v2.7.11b with parameters: sjdbOverhang 149 outSAMtype BAM SortedByCoordinate twopassMode Basic Aligned reads were summarised to the gene level using Subread featureCounts v2.0.6 with parameters: p countReadPairs fracOverlap 1 minOverlap 35 Assembly: GRCz11 Supplementary files format and content: Processed data contains gene level counts as output by featureCounts in TSV format.	Whole brain		RNA was extracted from whole brain tissue using Qiagen RNeasy columns. Stranded polyA libraries prepared according to the Nugen Universal Plus mRNA seq protocol and included 13 cycles of amplification.		tissue:Whole brain\|genotype:chr17 W233fs/+; chr14 PK/PK\|batch:1	GSM8785377	GSM8785377: Whole brain chr17 W233fs/+ chr14 PK/PK rep3; Danio rerio; RNA Seq	GSM8785377 r1	GSM8785377	1	RNA was extracted from whole brain tissue using Qiagen RNeasy columns. Stranded polyA libraries prepared according to the Nugen Universal Plus mRNA seq protocol and included 13 cycles of amplification.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP563065			SAGCFN_23_00422_S26_R1_001.fastq.gz SAGCFN_23_00422_S26_R2_001.fastq.gz	fastq fastq	12735641800.0	63678209.0	GSM8785377 r1	0:100 1:100	A:3422715945;C:2926637949;G:2924262666;T:3461837994;N:187246	100	100	3422715945	2926637949	2924262666	3461837994	187246	SRX27639470	SRS24046085	SRA2076182	The University of Adelaide	The University of Adelaide												B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	Australia	2025-02-10	Undetermined	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");;