run_metadata: 36356

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
36356	SRR372787	SRX107383	SRS280823	SRP009426	PRJNA154389	Comprehensive identification of long non coding RNAs expressed during zebrafish embryogenesis [RNA seq]	GSE32898	Transcriptome Analysis	Long non coding RNAs lncRNAs comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome wide studies in human and mouse have annotated lncRNAs expressed in cell lines and adult tissues but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis we performed a time series of RNA Seq experiments at eight stages during early zebrafish development. We reconstructed 56 535 high confidence transcripts in 28 912 loci recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1 133 non coding multi exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs lincRNAs intronic overlapping lncRNAs exonic antisense overlapping lncRNAs and precursors for small RNAs sRNAs. Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length low exon number low expression and conservation levels comparable to introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than protein coding genes and are specifically enriched in early stage embryos. In addition several lncRNAs show tissue specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions ranging from cell cycle regulation to morphogenesis. Our study provides the first comprehensive identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic genomic and evolutionary studies. Overall design: RNA Seq for 8 zebrafish developmental stages 2 lanes for each stage 3 for shield.	parent bioproject:PRJNA146503	pubmed:22110045;pubmed:23698349		2 4cell 1	GSM831503		source name:2 4cell RNA Seq\|tissue:embryo\|developmental stage:embryogenesis: 2 4 cell stage\|stdev for insert size:1336.039246	2 4cell 1	Th summary result files of he developmental transcriptome of all samples are available as supplementary information with the paper.	2 4cell RNA Seq		Total RNA was isolated using the standard Trizol Invitrogen protocol. Two rounds of PolyA+ RNA purification were performed for each sample using the PolyAPuristTM MAG kit Ambion. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand specific libraries for 76 bp paired end sequencing were prepared according to a modified UTP method Parkhomchuk et al. 2009 as detailed in Levin et al. 2010.	Zebrafish embryos were dechorionated at the 1 cell stage followed by incubation at 28C.	tissue:embryo\|developmental stage:embryogenesis: 2 4 cell stage\|average insert size fragment length:710.502832\|stdev for insert size:1336.039246	GSM831503	GSM831503: 2 4cell 1	GSM831503: 2 4cell 1	GSM831503: 2 4cell 1	1		GEO Accession:GSM831503	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP009426					6454083552.0	42461076.0	GSM831503 1	0:76 1:76	A:1659789336;C:1511027834;G:1564153032;T:1683582419;N:35530931	76	76			1659789336	1511027834	1564153032	1683582419	35530931	SRX107383	SRS280823	SRA048184	GEO	Sandelin, Dep. of Biology, University of Copenhagen	2	0.82115	0.94097	0.02927	0.02775	0.84362	0.79864	0.49872	0.49708	76	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		Denmark	2011-11-11	Cleavage	Embryo	Embryo Imprecise	All anatomical structures