{"database": "metadata", "table": "run_metadata", "rows": [[26474, "SRR25917889", "SRX21637652", "SRS18807741", "SRP458896", "PRJNA1013345", "Transcriptome analysis of zebrafish models of familial Alzheimer's disease and Sanfilippo syndrome childhood dementia display effects in common on the lysosome  oxidative phosphorylation and the ribosome", "GSE242370", "Transcriptome Analysis", "Here  we use intra family analysis to compare the gene expression profiles of one of our zebrafish models of EOfAD; psen1Q96 K97del and our model of Sanfilippo syndrome MPS IIIB  nagluA603fs  in young adult brains 6 month of age. We identified distinct changes to gene expression in each model at both ages. However  important commonalities were also observed  pointing to fundamental  underlying similarities in pathological mechanisms. Our findings highlight the potential of zebrafish models as valuable tools for investigation of neurodegenerative diseases. Overall design: We crossed a psen1Q96 K97del/+ ; nagluA603fs/+ zebrafish with a psen +/+ ; nagluA603fs/+ zebrafish  to generate a family of 100 sibling zebrafish with a number of various genotypes. We raised the entire family of fish until 6 month of age in shared environments 4 tanks side by side in the same recirculating water system. Then  the entire was euthanised by cold water shock. Each fish was genotyped  then n = 8 fish per wild type  EOfAD like psen1 Q96 K97del heterozygous and MPS IIIB naglu A603fs homozygous genotype were selected for RNAseq of their brain RNA", null, null, null, "22 02925", "GSM7761825", null, "source name:whole brain|tissue:whole brain|genotype:EOfAD like|Sex:female|hometank:3|rin:8.7|geo loc name:missing|collection date:missing", "22 02925", "fastp was used to trim adaptors and filter the reads by quality and length reads were aligned to the zebrafish genome GRCz11  Ensembl release 104 using STAR PCR duplicates were de duplicated using the dedup function of umi tools The number of reads aligning to gene models of the GRCz11 genome were counted using featureCounts Assembly: GRCz11  Ensembl release 104 Supplementary files format and content: csv file containing the output from featurecounts raw counts", "whole brain", null, "RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "tissue:whole brain|genotype:EOfAD like|Sex:F|hometank:3|rin:8.7", "GSM7761825", "GSM7761825: 22 02925; Danio rerio; RNA Seq", "GSM7761825 r1", "GSM7761825", "1", "RNA was extracted using the Qiagen Rneasy mini kit  then DNase treated using the DNAfree kit Libraries were generated according to the Nugen Universal Plus mRNA seq protocol and included 11 cycles of amplification. Libraries were all a similar size and quantity", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP458896", null, "loader:fastq load.py", "22-02925_S2_L01_R1_001.fastq.gz 22-02925_S2_L01_R2_001.fastq.gz", "fastq fastq", 1648026212.0, 8408297.0, "GSM7761825 r1", "0:98 1:98", "A:446399368;C:374586860;G:374491332;T:451683865;N:864787", 98, 98, null, null, 446399368, 374586860, 374491332, 451683865, 864787, "SRX21637652", "SRS18807741", "SRA1706756", "The University of Adelaide", "The University of Adelaide", 2, 0.92802, 0.92032, 0.11753, 0.11787, 0.7021, 0.70187, 0.49703, 0.49712, 98, 98, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-09-05", "Undetermined", "Undetermined", "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": ["26474"], "units": {}, "query_ms": 8.831774001009762}