{"database": "metadata", "table": "run_metadata", "rows": [[72028, "SRR22193367", "SRX18171775", "SRS15670997", "SRP406332", "PRJNA898346", "Comparison of the effects of mutaions modelling early onset familial Alzheimer's disease and Sanfilippo syndrome childhood dementia in zebrafish larvae", "GSE217196", "Transcriptome Analysis", "Neural cells are under immense pressure to maintain proper degradation of molecules using their endo lysosomal pathway ELP. In Alzheimer's disease AD  the gradual cognitive worsening of this age related disorder is partially due to dysfunction of the ELP. However  AD is a complex disorder and how the genetic landscape eventually leads to AD is unclear. Sanfilippo syndrome childhood dementia mucopolysaccharidosis type III  MPSIII is an extreme consequence of ELP dysfunction  where inherited recessive mutations result in the inability to properly catabolise a particular polysaccharide  which ultimately accumulates and interferes with the function of the ELP. Unlike AD  Sanfilippo is genetically simple all causative genes are identified. The primary biochemical consequences are understood and animal models of Sanfilippo are considered excellent models of the human disease. Since Sanfilippo and AD show similar pathological changes  they likely share disease associated mechanisms. Here  we dissect the similarity between AD and Sanfilippo using RNA seq. We have generated zebrafish knock in models of both diseases: the early onset familial AD like EOfAD like mutation psen1 Q96 K97del  and the MPSIII like mutation naglu A603fs. We generated a family of zebrafish containing wild type  heterozygous EOfAD like and homozygous MPSIII like genotypes. We raised the family until 7 dpf and performed mRNA seq on n = 8 induvial larvae per genotype. A power calculation revealed that this experiment was only contained 50% power to detect differentially expressed genes. Nevertheless  changes to the expression of genes encoding proteins involved in lysosomal function could be detected in the MPS III mutant larvae  suggesting a homeostatic response as the cells which make up the larval RNA seq samples respond to dysfunctional lysosomes. Overall design: We first paired fish a female zebrafish with genotype psen1 Q96 K97del/+ ; naglu A603fs/+ with a male zebrafish with genotype psen1 +/+ ; naglu A603fs/+. This gave a large family of > 100 sibling larvae with various psen1 and naglu genotypes. We raised the family of sibling larvae together in a large petri dish until 7 dpf The  the entire family was euthanised using an ice slurry. Individual larvae were placed in individual microfuge tubes containing 100 \u00b5L of RNAlater solution. Samples were then incubated in the RNAlater solution overnight at 4\u00b0C. Then  the tail from each larvae was cut from the rest of the head at the end of the yolk sac extension. The tail piece was used for genomic DNA extraction and PCR genotyping. The head was placed back in RNAlater. Once each larvae was genotyped for psen1 and naglu mutations  a total of 24 individual larvae were used for RNA extraction and sequencing: n = 8 wild type larvae  n = 8 EOfAD like/+ larvae and n = 8 MPS IIIB homozygous larvae.", null, "pubmed:36945478;pubmed:38346074", null, "MPS IIIB 21 01549", "GSM6706466", null, "source name:whole larvae|tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf", "MPS IIIB 21 01549", "98bp paired end sequencing + 8bp UMI using MGI DNBSEQ G400 chemistry Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors. Trimmed reads were aligned to the zebrafish genome Ensembl release GRCz11.101 using STAR v2.7.0d Alignments were counted using featureCounts subread v2.0.1 UMIs in the header of the fastq files were deduplicated from the alignments using umi tools v1.0.1 Assembly: GRCz11 release 101 Supplementary files format and content: raw counts output from featurecouunts", "whole larvae", "whole larvae were treated with RNAlater solution to stabilise RNA.", "Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion  Life Technologies  Thermo Fisher Scientific  Waltham  MA  USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion  Life Technologies  Thermo Fisher Scientific  Waltham  MA  USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508  protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit  Part No. MGI1000004155", "The larvae were raised in E3 medium for 7 days  allowing complete larval yolk absorption but not food intake", "tissue:whole larvae|genotype:MPS IIIB|developmental stage:7 dpf", "GSM6706466", "GSM6706466: MPS IIIB 21 01549; Danio rerio; RNA Seq", "GSM6706466 r1", "GSM6706466", "1", "Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit Ambion  Life Technologies  Thermo Fisher Scientific  Waltham  MA  USA. DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA freeTM Kit Ambion  Life Technologies  Thermo Fisher Scientific  Waltham  MA  USA. Only Stranded polyA libraries prepared by the South Australian Genomics Center SAGC using Nugen Universal Plus mRNA seq Part No. 0508  protocol M01442 v2. Then underwent Illumina to MGI Library Conversion MGIEasy Universal Library Conversion Kit  Part No. MGI1000004155", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP406332", null, "loader:fastq load.py", "21-01549_S1_4_R1_001.fastq.gz 21-01549_S1_4_R2_001.fastq.gz", "fastq fastq", 3950836340.0, 17958347.0, "GSM6706466 r4", "0:98 1:122", "A:952986092;C:906017140;G:1005513937;T:1085871362;N:447809", 98, 122, null, null, 952986092, 906017140, 1005513937, 1085871362, 447809, "SRX18171775", "SRS15670997", "SRA1534778", "The University of Adelaide", "The University of Adelaide", 2, 0.94349, 0.1071, 0.09625, 0.00814, 0.66691, 0.87428, 0.47077, 0.50094, 98, 122, "B", "T", "mate2 technical by mapping diff", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2022-11-03", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "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": ["72028"], "units": {}, "query_ms": 22.82502299931366}