run_metadata: 32042
This data as json
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| 32042 | SRR28992916 | SRX24520254 | SRS21267943 | SRP506997 | PRJNA1110229 | Zebrafish models of candidate human epilepsy associated genes provide evidence of hyperexcitability | PRJNA1110229 | 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 81 were determined suitable for the generation of loss of function zebrafish models via CRISPR/Cas9 gene editing. Of those 81 crispants 48 were successfully established as stable mutant lines and assessed for seizure like swim patterns in a primary F2 screen. Evidence of seizure like behavior was present in 5 arfgef1 kcnd2 kcnv1 ubr5 wnt8b of the 48 mutant lines assessed. Further characterization of those 5 lines 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. Furthermore RNAseq 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. | Wnt8b Hom3 | strain:Casper|age:5dpf|collection date:2022 12 09|geo loc name:USA: Boston MA|sex:not applicable|tissue:Head|genotype:Wnt8b Hom3|BioSampleModel:Model organism or animal | RNA Seq of Danio Rerio: pools of isolated larval head | Wnt8b Hom3 | Wnt8b Hom3 | 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. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP506997 | Wnt8b_Hom3.fq.gz | fastq | 5283928950.0 | 35226193.0 | Wnt8b Hom3.fq.gz | 0:150 | A:1389228037;C:1262004726;G:1265392219;T:1367105548;N:198420 | 150 | 1389228037 | 1262004726 | 1265392219 | 1367105548 | 198420 | SRX24520254 | SRS21267943 | SRA1863814 | Boston Childrens Hospital|Neurobiology | Boston Childrens Hospital | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2024-05-10 | Larval | Larval | Head | Nervous System |