run_metadata: 43060

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
43060	SRR8354697	SRX5165476	SRS4174522	SRP114782	PRJNA397065	mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis	PRJNA397065	Other	RNA folding plays a crucial role in RNA function. However our knowledge of the global structure of the transcriptome is limited to steady state conditions hindering our understanding of how RNA structure dynamics influences gene function. Here we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast we find that three prime UTRs form highly folded structures in vivo which can affect gene expression by modulating miRNA activity. Furthermore we find that dynamic three prime UTR structures are enriched in RNA decay elements including regulatory elements in nanog and cyclin A1 key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.				Raw multiplex: DMS seq RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2	Raw multiplex: DMS seq RNA positives ctrl in vitro B1 AG01489;DMS seq RNA positives ctrl in vitro B2 AG01490		strain:TU/AB\|age:3.7\|dev stage:oblong\|sex:pooled male and female\|tissue:embryo\|treatment:0.5% DMS for 10 min in vitro\|molecule:RNA\|condition:invitro DMS\|replicate group:1\|replicate:1;2\|barcode:TCTC;GTGT\|BioSampleModel:Model organism or animal									Raw multiplex: DMS seq RNA structure positive controls in vitro replicate 1;DMS seq RNA structure positive controls in vitro replicate 2	AG01489.1;AG01490.1	AG01489.1;AG01490.1	RNA			OTHER	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114782			C7MYYANXX_JBDX127_009_R1.fastq.gz	fastq	1115150128.0	14673028.0	C7MYYANXX JBDX127 009 R1.fastq.gz	0:76	A:313482382;C:276309346;G:291633361;T:233659719;N:65320	76				313482382	276309346	291633361	233659719	65320	SRX5165476	SRS4174522	SRA825010	Yale_Giraldez\|Genetics	Yale_Giraldez_Group	1	0.00546		0.00047		0.98602		0.51535		76		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	small_rna	unknown	bulk	unknown	unknown		United States	2018-12-19	Blastula	Embryo	Embryo Imprecise	All anatomical structures