{"database": "metadata", "table": "run_metadata", "rows": [[33701, "SRR30599780", "SRX26022471", "SRS22594190", "SRP531514", "PRJNA1158727", "CRISPR/Cas9 induced  zebrafish mutants for ebf3a and dhx30", "GSE276705", "Transcriptome Analysis", "Mutations in the transcription factor EBF3 results in a neurodevelopmental disorder  and studies in animal models indicate that it has a critical role in neuronal differentiation. The molecular pathways and neuron types disrupted by its loss  however  have not been thoroughly investigated. Nor have the outcomes of these changes on behavior and brain activity. Here  we generated and characterized a zebrafish ebf3a loss of function mutant. We discovered morphological and neural phenotypes  including an overall smaller brain size  particularly in the hypothalamus  cerebellum  and hindbrain. Brain function was also compromised  with activity strongly increased in the cerebellum and abnormal behavior at baseline and in response to visual and acoustic stimuli. From RNA sequencing of developing larvae  notable changes included significant downregulation of genes that mark olfactory sensory neurons  the lateral line  and cerebellar Purkinje neurons. This study sets the stage for determining which downstream pathways underlie the emergence of the observed phenotypes and establishes multiple strong phenotypes that could form the basis of a drug screen. Overall design: Total RNA was extracted from the anterior half of the body from 10 dpf 12 dpf 5 dpf larvae per sample at using the Rneasy Mini Kit Qiagen.  RNA for the 2 dpf RNA seq samples were collected in the same way  but with 15 20 embryos per pool. The 5 dpf RNA seq was collected also with 10 12 larvae. The posterior portion of the cuts was used for genotyping. The RNA was isolated from the anterior portion as described and submitted to sequencing by GENEWIZ at Azenta Life Sciences.", null, null, null, "ebf3a wt  2 dpf  rep 1", "GSM8504323", null, "source name:upper body with eyes  15 20 embryos pooled|tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types|geo loc name:missing|collection date:missing", "ebf3a wt  2 dpf  rep 1", "Paired end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. The raw counts files from STAR  in this record  were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.", "upper body with eyes  15 20 embryos pooled", null, "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "tissue:upper body with eyes|age:2 dpf|genotype:ebf3a wild types", "GSM8504323", "GSM8504323: ebf3a wt  2 dpf  rep 1; Danio rerio; RNA Seq", "GSM8504323 r1", "GSM8504323", "1", "Total RNA was extracted from the anterior half of the body from larvae per sample at using the Rneasy Mini Kit Qiagen. 10 12 for 6 dpf and 15 20 for 2 dpf. Libraries were constructed by GENEWIZ Azenta with standard protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP531514", null, null, "Ebf-WT-1-2dpf_R1_001.fastq.gz Ebf-WT-1-2dpf_R2_001.fastq.gz", "fastq fastq", 19711425600.0, 65704752.0, "GSM8504323 r1", "0:150 1:150", "A:5541464229;C:4291380685;G:4497372769;T:5380954703;N:253214", 150, 150, null, null, 5541464229, 4291380685, 4497372769, 5380954703, 253214, "SRX26022471", "SRS22594190", "SRA1966071", "UMass Chan Medical School", "UMass Chan Medical School", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2024-09-09", "Hatching", "Embryo", "Multi-tissue", "Multi-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": ["33701"], "units": {}, "query_ms": 8.490938998875208}