run_metadata: 36732

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
36732	SRR836198	SRX272887	SRS417393	SRP021915	PRJNA200706	Ribosome Profiling over a Zebrafish Developmental Timecourse	GSE46512	Transcriptome Analysis	To experimentally validate the non coding status of annotated lncRNAs we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell 256 cell 1K cell Dome Shield Bud 28hpf and 5dpf		pubmed:23698349		20120724 RPF Seq 28hpf	GSM1131536		tissue:Whole embryos\|developmental stage:28 hpf molecule:ribosome footprinted RNA	20120724 RPF Seq 28hpf	Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2 N 1 L 20 k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels no novel junctions M g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs +13 for 29 31nt RPFs +13 for 29 31nt RPFs +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes	Whole embryos	Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5°C and staged according to Kimmel et al. Dev. Dyn. 1995	developmental stage:28 hpf molecule:ribosome footprinted RNA	GSM1131536	GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq	GSM1131536 1		1	Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4 250 mM NaCl 15 mM MgCl2 1mM dithiothreitol 100 μg/ml cycloheximide with added 0.5% Triton X 100 500 μg/ml GMP PNP 24 U/ml TurboDNase Ambion AM2238 incubated with agitation for 10 min at 4°C and clarified by centrifugation at 1300 rcf for 10 min at 4°C. 20μl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37°C then stopped by chilling on ice and addition of 40 μl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4°C and resuspended in 800 μl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011	GEO Accession:GSM1131536	RNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP021915			20120724_RPF-Seq_28hpf.fastq.gz	fastq	5844769480.0	132835670.0	GSM1131536 r1	0:44	A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061	44				967687923	1803414766	2048220630	1024594100	852061	SRX272887	SRS417393	SRA075002	GEO	Schier, Dept of Molecular and Cellular Biology, Harvard University	1	0.054		0.00377		0.99762		0.77752		44		B		usable mapping rate	illumina	hiseq_era	5prime	size_fractionation	unknown	bulk	unknown	unknown		United States	2013-04-30	Pharyngula	Embryo	Whole Organism	All anatomical structures