run_metadata: 75369

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
75369	SRR24489438	SRX20274782	SRS17602473	SRP436765	PRJNA970658	Transcriptome analysis of Cygb1 Knockout in Zebrafish Danio rerio	PRJNA970658	Other	Cytoglobin Cygb is an evolutionary ancient heme protein with yet unclear physiological functions. Cygb might be involved in ROS detoxification NO metabolism and lipid based signaling processes. Mammalian Cygb is ubiquitously expressed in all tissues. We used a CRISPR/Cas9 genome editing approach and generated a knockout of the penta coordinated cygb1 for in vivo analysis in zebrafish. Adult cygb1 knockouts develop phenotypic anomalies including neoplasia of gonads and weight loss. To identify the molecular mechanisms underlying the occurrence of these phenotypes and differentiate between function and effect of the knockout we compared the transcriptomes of cygb1 knockouts at different ages to age matched wild type WT zebrafish.				Old KO Brain 2	Cygb1KO G 2 S29 R1 001		strain:Tuebingen\|isolate:Brain 2 Cygb1KO\|age:24 mpf\|dev stage:adult\|sex:male\|tissue:brain\|genotype:cygb1 knockout\|BioSampleModel:Model organism or animal									RNAseq Zebrafish 24mpf Brain Cygb1KO	Cygb1KO G 2S29	Cygb1KO G 2S29	Total RNA was extracted using the Crystal RNA Mini Kit following the instructions of the manufacturer. RNA samples were treated with DNaseI Qiagen according to the manufacturers protocol. RNA concentration and quality for Illumina sequencing was measured by employing the TapeStation System 2200. A library for paired end sequencing was generated from 1 g total RNA.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP436765			Cygb1KO-G-2_S29_R1_001.fastq.gz Cygb1KO-G-2_S29_R2_001.fastq.gz	fastq fastq	9228083087.0	31353095.0	Cygb1KO G 2 S29 R1 001.fastq.gz	0:146.81 1:147.51	A:2685482962;C:1925153227;G:1961258559;T:2654447279;N:1741060	146	147			2685482962	1925153227	1961258559	2654447279	1741060	SRX20274782	SRS17602473	SRA1634682	University of Hamburg\|Institute of Animal Cell and Systems Biology (IZS)	University of Hamburg	2	0.94076	0.94161	0.20564	0.20278	0.70498	0.70157	0.51187	0.51437	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		Germany	2023-05-10	Adult	Adult	Brain	Nervous System