run_metadata: 11740

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
11740	ERR11422860	ERX10830031	ERS15422315	ERP147133	PRJEB62042	RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein	E-MTAB-12934	Transcriptome Analysis	RNA seq of zebrafish embryos with mutations in srpk3 sa1890 allele and/or ttn.1 sa5562 allele. Each of the 24 samples six samples for each of four genotypes represents RNA from a pool of three 5 dpf zebrafish embryos.	ENA FIRST PUBLIC:2024 02 09\|ENA LAST UPDATE:2024 02 09		Protocols: Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.	srpk3 wt ttn1 wt 4	SAMEA113427189	QMUL	ENA FIRST PUBLIC:2024 02 09T16:00:07Z\|ENA LAST UPDATE:2024 02 09T16:00:07Z\|External Id:SAMEA113427189\|INSDC center name:QMUL\|INSDC first public:2024 02 09T16:00:07Z\|INSDC last update:2024 02 09T16:00:07Z\|INSDC status:public\|Submitter Id:E MTAB 12934:srpk3 wt ttn1 wt 4\|age:5\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:embryo\|genotype:srpk3 +/+; ttn.1 +/+\|individual:pool of 3 embryos 4\|organism part:embryo\|replicate:4\|sample name:E MTAB 12934:srpk3 wt ttn1 wt 4\|scientific name:Danio rerio\|sex:not available\|strain:Tüpfel long fin									RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein	E MTAB 12934:srpk3 wt ttn1 wt 4 p	srpk3 wt ttn1 wt 4 p	RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein	Zebrafish embryos were collected for DNA and RNA extraction at 5 dpf in 6 pools of 3 embryos per genotype. Samples were lysed in 110 μl RLT buffer Qiagen containing 1.1 μl of 14.3 M β mercaptoethanol Sigma. The lysate was allowed to bind to 450 μl of Agencourt AMPure XP beads Beckman Coulter for 15 minutes. The tubes were left on a magnet Invitrogen until the solutions cleared and the supernatant was then removed without xxx the beads. Whilst still on the magnet the beads were washed three times with 70% ethanol and allowed to dry for 20 minutes. Total nucleic acid was eluted from the beads following the manufacturer's instructions and treated with DNase I NEB Catalog number M0303L. NEBNext Ultra II DNA Library Prep Kit for Illumina.	Experimental Factor: genotype:srpk3 +/+; ttn.1 +/+	RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP147133	Illumina NovaSeq 6000 paired end sequencing; RNA seq of zebrafish embryos with mutations in a muscle specific kinase and the giant titin protein	ENA FIRST PUBLIC:2024 02 09\|ENA LAST UPDATE:2024 02 09	SLX-21419.H4.HV2TTDRXY.s_2.r_1.fq.gz SLX-21419.H4.HV2TTDRXY.s_2.r_2.fq.gz	fastq fastq	8552416200.0	28508054.0	E MTAB 12934:SLX 21419.H4.HV2TTDRXY.s 2.r	0:150 1:150	A:2292742388;C:1992671634;G:2031906776;T:2234679447;N:415955	150	150			2292742388	1992671634	2031906776	2234679447	415955	ERX10830031	ERS15422315	ERA23329494	European Bioinformatics Institute\|European Nucleotide Archive	European Bioinformatics Institute\|European Nucleotide Archive												B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	nebnext	bulk	unknown	unknown		United Kingdom	2024-02-09	Larval	Larval	Embryo Imprecise	All anatomical structures