run_metadata: 33699

This data as json

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
33699	SRR30599778	SRX26022473	SRS22594192	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.				ebf3a hom 5 dpf rep 1	GSM8504325		source name:head with eyes 10 12 embryos pooled\|tissue:head with eyes\|age:5 dpf\|genotype:ebf3a homozygous\|geo loc name:missing\|collection date:missing	ebf3a hom 5 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.	head with eyes 10 12 embryos pooled		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		tissue:head with eyes\|age:5 dpf\|genotype:ebf3a homozygous	GSM8504325	GSM8504325: ebf3a hom 5 dpf rep 1; Danio rerio; RNA Seq	GSM8504325 r1	GSM8504325	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		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP531514			Ebf-Homo-1-5dpf_R1_001.fastq.gz Ebf-Homo-1-5dpf_R2_001.fastq.gz	fastq fastq	16257229800.0	54190766.0	GSM8504325 r1	0:150 1:150	A:4127739980;C:3994508761;G:4048290353;T:4086361510;N:329196	150	150			4127739980	3994508761	4048290353	4086361510	329196	SRX26022473	SRS22594192	SRA1966071	UMass Chan Medical School	UMass Chan Medical School												B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2024-09-09	Larval	Larval	Multi-tissue	Multi-system