run_metadata: 28432

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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. We chose n = 6 as according to a previous power calculation this would allow approximately 70% power to detect differentially expressed genes in zebrafish models of Alzheimer's disease. However due to smaller than expected clutch sizes and questionable purified RNA quality we were forced to use multiple families of siblings or n<6 in some analyses. For the A and B AB arm of the experiment we analysed n = 4 fish per genotype which also included 4 sgsh S387Lfs/+ fish to explore cellular processes affected in the brains of presumably unaffected carriers of MPS III mutations. For the A and C AC arm we sequenced all homozygous sgsh S387Lfs zebrafish in the family n = 7 to account for the lower number of fish with this genotype in the AB arm. For the B and C BC arm we could not obtain a large enough family in a single breeding event within our timeframe to be able to compare with the other families. Therefore we analysed fish spawned by two pairs of parents P1 and P2 both doubly heterozygous for the nagluA603fs and hgsnatG577fs mutations in a total of 3 spawning events.				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