run_metadata: 15400

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
15400	ERR12724516	ERX12099015	ERS18400120	ERP158370	PRJEB73599	RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings	E-MTAB-13886	Transcriptome Analysis	Bulk tissue RNA sequencing of individual 24hpf zebrafish larvae to compare the gene expression values between wild type and foxg1a nonsense mutants heterozygous and homozygous mutants. The mutation is a 5bp deletion 32bp from canonical start codon; AAATG deleted.	ENA FIRST PUBLIC:2024 03 29\|ENA LAST UPDATE:2024 03 29		Protocols: Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.	Foxg1 WT 1	E MTAB 13886:Foxg1 WT 1		isolate:not applicable\|organism:Danio rerio\|organism:Danio rerio\|collection date:not collected\|scientific name:Danio rerio\|common name:zebrafish\|organism part:whole organism\|developmental stage:pharyngula prim 5\|genotype:Foxg1a WT\|geographic location country and/or sea:not collected									RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings	E MTAB 13886:Foxg1 WT 1 p	Foxg1 WT 1 p	RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings	Heterozygous mutant 5bp deletion 32 bp from canonical start codon; AAATG foxg1a adult zebrafish in a dlx5 6;GFP background were incrossed and progeny collected. Dlx+ interneuron phenotype was used to identify homozygous no interneurons in telencephalon and heterozygous reduced number of interneurons in telencephalon. Genotyping was confirmed with RNA sequencing reads at the foxg1a gene locus to ensure correct genotyping. RNA was extracted from single 24hpf zebrafish using the Qiagen RNeasy Micro Kit Qiagen 74004. RNA concentration was measured using the Qubit reagent kit and a small sample was tested for RNA integrity using a bioanalyzer instrument. Only samples with an RNA integrity number of 9 or above were used in this experiment. Total RNA Library was repapred using the Illumina TruSeq Stranded Total RNA Library kit. Ribosomal RNAs were depleted using Ribo Zero Gold.		RNA-Seq	TRANSCRIPTOMIC	Inverse rRNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP158370	Illumina NovaSeq 6000 paired end sequencing; RNA seq of 24hpf Zebrafish larvae comparing foxg1a mutants to WT siblings	ENA FIRST PUBLIC:2024 03 29\|ENA LAST UPDATE:2024 03 29	18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R1_001.fastq.gz 18067X13_200629_A00421_0211_BHN23CDRXX_S14_L001_R2_001.fastq.gz	fastq fastq	4252867662.0	41694781.0	E MTAB 13886:18067X13 200629 A00421 0211 BHN23CDRXX S14 L001 R	0:51 1:51	A:1069523245;C:1031533375;G:1047047746;T:1104513602;N:249694	51	51			1069523245	1031533375	1047047746	1104513602	249694	ERX12099015	ERS18400120	ERA29264914	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	rrna_depletion	trueseq	bulk	bulk	bulk		United Kingdom	2024-03-29	Pharyngula	Embryo	Whole Organism	All anatomical structures