{"database": "metadata", "table": "run_metadata", "rows": [[32084, "SRR29007573", "SRX24534619", "SRS21280302", "SRP507312", "PRJNA1111077", "Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability", "PRJNA1111077", "Other", "Hundreds of novel candidate human epilepsy associated genes have been identified thanks to advancements in next generation sequencing and large genome wide association studies  but establishing genetic etiology requires functional validation. We generated a list of >2200 candidate epilepsy associated genes  of which 48 were developed into stable loss of function zebrafish models. Of those 48  evidence of seizure like behavior was present in 5 arfgef1  kcnd2  kcnv1  ubr5  wnt8b. Further characterization provided evidence for epileptiform activity via electrophysiology in kcnd2 and wnt8b mutants. Additionally  arfgef1 and wnt8b mutants showed a decrease in the number of inhibitory interneurons in the optic tectum of larval animals. Further  RNA Seq revealed convergent transcriptional abnormalities between mutant lines  consistent with their developmental defects and hyperexcitable phenotypes. These zebrafish models provide strongest experimental evidence supporting the role of ARFGEF1  KCND2  and WNT8B in human epilepsy and further demonstrate the utility of this model system for evaluating candidate human epilepsy genes.", null, null, null, null, "Wnt8b Wt 1", null, "strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston  MA|sex:not applicable|tissue:Head|genotype:Wnt8b Wt1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio Rerio: pools of isolated larval head", "Wnt8b Wt 1", "Wnt8b Wt 1", "Three replicate larvae from Het in crosses  aged 5 dpf  were sacrificed on ice and stored in RNAlater Stabilization Solution according to product specifications. Larval heads were isolated from bodies  which were used for Sanger sequencing for genotyping. Heads were pooled in groups of 20 25 according to genotype and RNA was isolated using a Qiagen RNeasy plus kit according to specifications. QC was performed via Agilent 2100 bioanalyzer  and only samples with an RNA integrity number value of >5.8 were used for library preparation.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP507312", null, null, "Wnt8b_Wt_1_1.fq.gz Wnt8b_Wt_1_2.fq.gz", "fastq fastq", 6534620400.0, 21782068.0, "Wnt8b Wt 1 1.fq.gz", "0:150 1:150", "A:1783250074;C:1493088330;G:1497228073;T:1760957638;N:96285", 150, 150, null, null, 1783250074, 1493088330, 1497228073, 1760957638, 96285, "SRX24534619", "SRS21280302", "SRA1864976", "Boston Childrens Hospital|Neurobiology", "Boston Childrens Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-05-13", "Larval", "Larval", "Head", "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": ["32084"], "units": {}, "query_ms": 11.777928000810789}