run_metadata: 9928

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
9928	ERR4321733	ERX4268591	ERS4808148	ERP122765	PRJEB39269	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/ß catenin signaling at the early wound healing stage	E-MTAB-9321	Transcriptome Analysis	Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing RNA Seq is a high throughput sequencing method facilitating quantification of gene expression in a precisely manner. Development of RNA Seq technologies and their extensive data analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. In this study we reveal the whole transcriptome profiles of both the lesioned and unlesioned hemispheres of the zebrafish telencephalon at early wound healing 20 hour post lesion and early proliferative 3 day post lesion stages of regeneration. Moreover we uncover Wnt/ß catenin signaling as a key pathway that is activated at the early wound healing stage.	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 06		Protocols: Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Ctrl uni R 2	SAMEA7047514	Izmir Biomedicine and Genome Center	ENA FIRST PUBLIC:2020 10 05T04:05:55Z\|ENA LAST UPDATE:2020 07 06T18:12:29Z\|External Id:SAMEA7047514\|INSDC center name:Izmir Biomedicine and Genome Center\|INSDC first public:2020 10 05T04:05:55Z\|INSDC last update:2020 07 06T18:12:29Z\|INSDC status:public\|Submitter Id:E MTAB 9321:Ctrl uni R 2\|age:6 to 10\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:6xTCF/Lef miniP:2dGFP\|organism part:telencephalon\|sample name:E MTAB 9321:Ctrl uni R 2\|sampling site:right cerebral hemisphere\|scientific name:Danio rerio\|sex:male									NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	E MTAB 9321:Ctrl uni R 2 p	Ctrl uni R 2 p	Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β catenin signaling at the early wound healing stage	Tissues were dissected under microscopy. Adult zebrafish were fed under normal conditions Dissected tissues were immersed in RNA later and Total RNA isolation was performed. RNA seq libraries were built using the TruSeq RNA Library Preparation v2 Kit Illumina	Experimental Factor: injury:n1\|Experimental Factor: compound:n1	RNA-Seq	TRANSCRIPTOMIC	other	PAIRED	ILLUMINA	NextSeq 500		ERP122765	NextSeq 500 paired end sequencing; Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/Î² catenin signaling at the early wound healing stage	ENA FIRST PUBLIC:2020 10 05\|ENA LAST UPDATE:2020 07 07	Ctrl_uni_R_2_1.txt Ctrl_uni_R_2_2.txt	fastq fastq	6922683200.0	43266770.0	E MTAB 9321:Ctrl uni R 2	0:80 1:80	A:1632897692;C:1799983634;G:1813073970;T:1675697152;N:1030752	80	80			1632897692	1799983634	1813073970	1675697152	1030752	ERX4268591	ERS4808148	ERA2763798	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	Izmir Biomedicine and Genome Center\|European Nucleotide Archive	2	0.9343	0.93678	0.30732	0.30767	0.77226	0.77496	0.67322	0.638	80	80	B	B	biological fallback assumption	illumina	nextseq	full_length	random_priming	trueseq	bulk	unknown	unknown		Turkey	2020-07-06	Adult	Adult	Brain	Nervous System