run_metadata: 37264

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
37264	SRR1049953	SRX392055	SRS515266	SRP034166	PRJNA231739	Silencing of odorant receptor gene expression by G protein ß? signaling ensures the expression of one odorant receptor per olfactory sensory neuron	GSE53334	Transcriptome Analysis	Olfactory sensory neurons express just one out of a possible 1000 odorant receptor genes reflecting an exquisite mode of gene regulation. In one model once an odorant receptor is chosen for expression other receptor genes are suppressed by a negative feedback mechanism ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover we show that signaling through G protein ß? subunits is both necessary and sufficient to suppress the expression of odorant receptor genes and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Overall design: Total 6 samples were analyzed 3 controls & 3 samples		pubmed:24559675;pubmed:25150836		Treated biological replicate 1	GSM1289433		tissue:Olfactory sensory neuron\|tansgenic line:OMP Gal4 transgenic zebrafish\|cell sorting:GFP +\|agent:100 µM gallein	Treated biological replicate 1	Illumina Casava1.7 software used for basecalling. Reads were mapped to a custom reference defined as the union of the Zv9 reference zebrafish genome downloaded from Ensembl v. 67 and the ERCC spike in sequences using TopHat v. 2.0.4 supplying the Ensembl GTF annotation through the G option Gene level read counts were generated using the htseq count python script in the "union" mode and Ensembl v. 67 gene annotation Genome build: Zv9 Supplementary files format and content: tab delimited text files contain gene level read counts for each sample	Olfactory sensory neuron	At 16 hpf 20 hpf embryos were treated with 100 µM gallein or DMSO control. Fresh embryo media with the appropriate drug treatment was replaced every 24 hours. Heads of 5 dpf embryos were dissected and dissociated with trypsin and collagenase and sorted for GFP fluorescence; cells were collected in 1ml of Trizol and stored at 80oC	Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer’s IntegenX Inc. protocols.	OMP Gal4;UAS GCaMP1.6 transgenic zebrafish embryos were collected upon fertilization and raised in embryo media at 28oC.	tansgenic line:OMP Gal4 transgenic zebrafish\|cell sorting:GFP +\|agent:100 µM gallein	GSM1289433	GSM1289433: Treated biological replicate 1; Danio rerio; RNA Seq	GSM1289433		1	Total RNA was harvested using Trizol reagent & DNase treated. PolyA+ RNA was enriched from total RNA using oligodT25 magnetic beads Life Technologies cat#61006. The libraries were prepared using PrepX SPIA RNA Seq cat#400030 and ILM DNA Library kits cat#400044 according to the manufacturer’s IntegenX Inc. protocols.	GEO Accession:GSM1289433	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP034166			TFJN03_TF9_index19_GTGAAA_L001_R2.fastq.gz TFJN03_TF9_index19_GTGAAA_L001_R1.fastq.gz	fastq fastq	5477198400.0	27385992.0	GSM1289433 r2	0:100 1:100	A:1526066704;C:1150303729;G:1233326927;T:1532243060;N:35257980	100	100			1526066704	1150303729	1233326927	1532243060	35257980	SRX392055	SRS515266	SRA116880	GEO	University of California, Berkeley	2	0.92412	0.87983	0.1198	0.11437	0.81874	0.82546	0.73064	0.72533	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		United States	2013-12-15	Multi-stage	Multi-stage	Brain	Nervous System