run_metadata: 41299

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
41299	SRR8173224	SRX4993777	SRS4029189	SRP168138	PRJNA340009	RNASeq of OMP and TRPC2 neuronal population of zebrafish olfactory sensory neurons	GSE86023	Transcriptome Analysis	RNASeq was performed on mRNA obtained from OMP expressing and TRPC2 expressing olfactory sensory neurons from 48hpf zebrafish embryos. Single cell suspensions of 48hpf olfactory epithelia were FAC sorted to obtain RFP expressing or venus expressing cells RFP sample1: 3500 cells RFP sample2: 5500 cells. Venus sample1: 676 cells venus sample2:201 cells. RNA was extracted using QIAGEN RNEasy kit and cDNA was synthesized using a custom oligo dT primer containing T7 promoter sequence courtesy of Jim Eberwine University of Pennsylvanina. In vitro RNA amplification was carried out through one round for OMP:RFP neurons and through two rounds for TRPC2:venus neurons as per the protocol in Morris et al 2011. Adapter tagged libraries were synthesized using Illumina TruSeq v2.0 and deep sequenced on HiSeq2500 to obtain 100million reads per sample. Overall design: Examination of mRNA expression profiles from 2 types of olfactory sensory neurons		pubmed:29020985		OMP 2	GSM2290759		tissue:OMP expressing olfactory sensory neurons\|strain:Tubingen/TLF\|embryo stage:48hpf\|cell type:olfactory sensory neurons\|neuron subtype:OMP	OMP 2	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped tozebrafish GRCz10 whole genome. Reads per millionrpm values were calculated by dividing the number of read counts for a gene by the total number of uniquely mapped reads in million for that sample. Alignment – STAR algorithm Gene counts – VERSE Genome build: Ensemble zebrafish assembly GRCz10 Supplementary files format and content: Comma separated text files include raw gene counts or gene counts in reads per million for each sample	OMP expressing olfactory sensory neurons	Olfactory epithelia were dissected and single cell suspensions were prepared using trypsin to dissociate the cells. Fluorescence assisted cell sorting FACS was used to obtain RFP only and venus only cell populations. Cells were collected in RNA lysis buffer.	Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.	Zebrafish embryos expressing OMP:RFP or TRPC2:venus were harvested and incubated at 28.5oC till 48hpf.	strain:Tubingen/TLF\|embryo stage:48hpf\|cell type:olfactory sensory neurons\|neuron subtype:OMP	GSM2290759	GSM2290759: OMP 2; Danio rerio; RNA Seq	GSM2290759		1	Total cellular RNA was extracted using Qiagen Rneasy micro kit. T7 oligodT primers were used for reverse transcription of mRNA during cDNA synthesis. RNA amplification was performed using T7 Megascript kit through one for OMP neurons two rounds for TRPC2 neurons. Illumina TruSeq v2.0 kit was used as per manufacturer's protocol.	GEO Accession:GSM2290759	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP168138			FGC0805_s_6_1_CTTGTA.fastq.gz FGC0805_s_6_2_CTTGTA.fastq.gz	fastq fastq	25768751000.0	128843755.0	GSM2290759 r1	0:100 1:100	A:6815152641;C:6065596177;G:5514207833;T:7360566579;N:13227770	100	100			6815152641	6065596177	5514207833	7360566579	13227770	SRX4993777	SRS4029189	SRA807287	GEO	Jonathan Raper, Neuroscience, University of Pennsylvania	2	0.94122	0.87325	0.12592	0.11103	0.7235	0.73563	0.4808	0.5167	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		United States	2016-08-24	Hatching	Embryo	Brain	Nervous System