run_metadata: 11181

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
11181	ERR10180594	ERX9716160	ERS13447536	ERP140949	PRJEB56027	Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress	E-MTAB-12172	Transcriptome Analysis	To identify the molecular pathways in the cryaba mutant by Nrf2 deficiency we performed high throughput transcriptome profiling on adult zebrafish lens and heart tissues from the WT cryaba / nrf2fh318/fh318 and cryaba / ;nrf2fh318/fh318 lines.	ENA FIRST PUBLIC:2022 09 24\|ENA LAST UPDATE:2022 09 24		Protocols: adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.	lens abaKO 1	SAMEA111349989	Vanderbilt Univiersity	ENA FIRST PUBLIC:2022 09 24\|ENA LAST UPDATE:2022 09 24\|External Id:SAMEA111349989\|INSDC center alias:Vanderbilt Univiersity\|INSDC center name:Vanderbilt Univiersity\|INSDC first public:2022 09 24T00:21:08Z\|INSDC last update:2022 09 24T00:21:08Z\|INSDC status:public\|Submitter Id:E MTAB 12172:lens abaKO 1\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:cryaba knockout\|organism part:lens\|sample name:E MTAB 12172:lens abaKO 1\|sex:male									Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress	E MTAB 12172:lens abaKO 1 p	lens abaKO 1 p	Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress	adult zebrafish lens tissues were dissected The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. Gupta T. and M.C. Mullins Dissection of organs from the adult zebrafish. J Vis Exp 201037. The following mutant and transgenic fish lines were used: cryabavu612 cryba / ; cryabbvu613 crybb / ; nrf2fh318. All animal procedures were approved by the Vanderbilt University Institutional Animal Care and Use Committee. RNA was extracted using a Trizol reagent with RNA clean up kit Zymo R2050 according to the manufacturer's instruction. Raw sequencing reads were obtained for the paired end samples.	Experimental Factor: genotype:cryaba knockout	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		ERP140949	Illumina NovaSeq 6000 paired end sequencing; Transcriptional coupling between Nrf2 and aB crystallin in the lens and heart of zebrafish under proteostatic stress	ENA FIRST PUBLIC:2022 09 24\|ENA LAST UPDATE:2022 09 24	5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R1_001.fastq.gz 5089-PP-3-AAGGCGTA-CCATCCGC_S01_L005_R2_001.fastq.gz	fastq fastq	18850381500.0	62834605.0	E MTAB 12172:5089 PP 3 AAGGCGTA CCATCCGC S01 L005 R	0:150 1:150	A:4831021904;C:4613611754;G:4712103573;T:4693153324;N:490945	150	150			4831021904	4613611754	4712103573	4693153324	490945	ERX9716160	ERS13447536	ERA17903080	Vanderbilt Univiersity\|European Nucleotide Archive	Vanderbilt Univiersity\|European Nucleotide Archive	2	0.94079	0.94389	0.04169	0.04008	0.82367	0.82524	0.4379	0.43771	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2022-09-24	Adult	Adult	Heart	Cardiovascular System