run_metadata: 56353

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
56353	SRR10951081	SRX7618052	SRS6050656	SRP243909	PRJNA602675	Identification of mecciRNAs and their roles in the mitochondrial entry of proteins	GSE144063	Other	To identify mitochondrial RNAs we isolated mitochondria and performed RNA sequencing. Differential expression of mRNAs and circRNAs were then analyzed. Overall design: RNA seq of Mitochondria		pubmed:32048164		Mitochondria of fish	GSM4278970		source name:whole fish\|tissue:whole fish	Mitochondria of fish	For circular RNA circRNA prediction we identified the candidates with find circ Memczak et al. 2013 and the junction reads were calculated as Transcripts Per Kilobase Million TPM. Genome build: hg19 mm9 danRer11 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...	whole fish		The isolated mitochondria were homogenized in TRizol reagent Life Technologies by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols		tissue:whole fish	GSM4278970	GSM4278970: Mitochondria of fish; Danio rerio; RNA Seq	GSM4278970		1	The isolated mitochondria were homogenized in TRizol reagent Life Technologies by homogenizer. Total RNA was extracted by using TRizol reagent according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4278970	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP243909			zb-mito_1.clean.fq.gz zb-mito_2.clean.fq.gz	fastq fastq	10952542200.0	36508474.0	GSM4278970 r1	0:150 1:150	A:2318277579;C:3207781428;G:3157469050;T:2269014143;N:0	150	150			2318277579	3207781428	3157469050	2269014143	0	SRX7618052	SRS6050656	SRA1029966	GEO	School of Life Sciences, University of Science and Technology of China	2	0.98468	0.98448	0.12861	0.13005	0.99555	0.99577	0.83968	0.8042	150	150	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		China	2020-01-22	Undetermined	Undetermined	Whole Organism	All anatomical structures