run_metadata: 41315

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
41315	SRR4199304	SRX2148084	SRS1679262	SRP087617	PRJNA342262	Proliferation independent regulation of organ size by Notch signaling	GSE86571	Transcriptome Analysis	Purpose: To identify genes that are transcriptionally controlled by Notch signaling during zebrafish lateral line proneuromast formation. Methods: We isolated primordium cells from dissected tails of 36 hpf TgcldnB:GFP;TgcldnB:gal4 x TgUAS:nicd and sibling TgcldnB:GFP;TgcldnB:gal4 embryos by FACS and performed RNASeq analysis. Results: Using an optimized data analysis workflow we mapped about 26 million sequence reads per sample to the zebrafish genome build danRer10 and identified 32 105 transcripts in the dissociated tails of WT and NICD zebrafish with TopHat workflow. Approximately 2% of the transcripts showed differential expression between the WT and NICD tails with a fold change =0.5 and p value <0.01. Conclusion: RNASeq analyses revealed that Notch signaling cell autonomously induces apical constriction and cell adhesion. Overall design: Zebrafish lateral line mRNA profiles of 36 hours wild type WT and NICD embryos were generated in triplicate using HiSeq 2500 Illumina.		pubmed:28085667		WT rep3	GSM2306084		source name:dissociated embryo tails\|strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	WT rep3	Illumina CASAVA 1.8.2 software used for basecalling. Sequenced reads were mapped to danRer10 whole genome using tophat v2.0.13 with parameters p 8 transcriptome index G o no coverage search The fragments per kilobase of transcript per million mapped reads FPKM values were generated using Cufflinks version 2.2.1 with parameters p 4 g o. Reads were counted on danRer10 Ensembl transcripts from UCSC using HTSeq version 0.6.1 with parameters m intersection nonempty s no f bam. Genome build: danRer10 from UCSC Supplementary files format and content: Two tab delimited text files: one includes raw counts of sequencing reads for each Sample one includes FPKM values for each Sample.	dissociated embryo tails	Zebrafish embryos positive for GFP were selected.	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	Zebrafish embryos were raised for 36 hpf in the 28.5C incubator.	strain:Tgcldnb:lynGFPzf106\|tissue:dissociated embryo tails\|age:36 hpf type	GSM2306084	GSM2306084: WT rep3; Danio rerio; RNA Seq	GSM2306084		1	Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#RS 122 2302 was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.	GEO Accession:GSM2306084	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP087617			WT3.fastq.gz	fastq	1621399650.0	31792150.0	GSM2306084 r1	0:51 1:0	A:394689371;C:400826196;G:384059217;T:441773624;N:51242	51	0			394689371	400826196	384059217	441773624	51242	SRX2148084	SRS1679262	SRA464955	GEO	Stowers Institute for Medical Research	1	0.87053		0.08236		0.7218		0.4831		51		B		usable mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown		United States	2016-09-08	Pharyngula	Embryo	Tail	Multi-system