run_metadata: 36279

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
36279	SRR352485	SRX100937	SRS266976	SRP008845	PRJNA146609	Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution	GSE32880	Other	Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs we used chromatin marks polyA site mapping and RNA Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs only 29 had detectable sequence similarity with putative mammalian orthologs typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3 H3K36me3 chromatin maps 3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome		pubmed:22196729		3P Seq 72 hpf	GSM813763		tissue:whole embryo at 72 hpf embryo\|developmental stage:72 hpf	3P Seq 72 hpf	Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924	whole embryo at 72 hpf	Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl 2.7 mM KCl 1.5 mM KH2PO4 8 mM Na2HP04 pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed and pellets were rinsed twice with PBS flash frozen in liquid nitrogen and stored at –80C.	3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html	Zebrafish embryos or adults grown under standard condition	tissue:whole embryo\|developmental stage:72 hpf	GSM813763	GSM813763: 3P Seq 72 hpf	GSM813763: 3P Seq 72 hpf	GSM813763: 3P Seq 72 hpf	1		GEO Accession:GSM813763	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina Genome Analyzer II	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP008845		read name barcode proc directive:ignore	3P_Seq_72hpf.fastq	fastq	875542968.0	24320638.0	GSM813763 1	0:36	A:246098313;C:139311840;G:129654215;T:353566279;N:6912321	36				246098313	139311840	129654215	353566279	6912321	SRX100937	SRS266976	SRA047033	GEO	Whitehead Institute for Biomedical Research	1	0.72092		0.09355		0.7601		0.4422		36		B		usable mapping rate	illumina	early_illumina	3prime	size_fractionation	unknown	bulk	unknown	unknown		United States	2011-10-11	Larval	Larval	Whole Organism	All anatomical structures