{"database": "metadata", "table": "run_metadata", "rows": [[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. 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.", null, null, null, "Brain  AB  WT  rep2 [22 00150 S6]", "GSM7813293", null, "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", null, "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 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen  Thermo Fisher Scientific  Waltham  USA overnight at 4\u00b0C  before storage at  80\u00b0C 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\u2122 miRNA Isolation Kit Ambion  Life Technologies  Thermo Fisher Scientific  Waltham  USA following the manufacturer\u2019s protocol. To remove any carried over genomic DNA during RNA purification  we treated the total RNA samples with DNaseI using the DNA free\u2122 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 \u2265 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 \u00b5l of RNAlater\u2122 Stabilization Solution Invitrogen  Thermo Fisher Scientific  Waltham  USA overnight at 4\u00b0C  before storage at  80\u00b0C 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\u2122 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\u2122 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 \u2265 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP463830", null, null, "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, null, null, 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", null, "Australia", "2023-09-29", "Adult", "Adult", "Brain", "Nervous System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["28452"], "units": {}, "query_ms": 8.678450998559128}