run_metadata: 40950

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
40950	SRR3465553	SRX1735455	SRS1416508	SRP074122	PRJNA319956	Gene expression data from NRAS driven CNS PNET zebrafish brain tumors and normal brain.	GSE80768	Transcriptome Analysis	Zebrafish CNS PNET tumors were generated by activating NRAS in oligoneural precursor cells. Gene expression in the zebrafish brain tumors and normal zebrafish brain was analyzed by RNA seq. Overall design: RNA seq was performed on 7 zebrafish brain tumors and 8 normal brain samples on Illumina HiSeq 2000 using 50 Cycle Single Read Sequencing v3 kit.		pubmed:27783941		9267X8 tumor	GSM2136821		source name:brain tumor\|tissue:brain tumor	9267X8 tumor	USeq’s MakeTranscriptome v8.8.8 application was used to create all possible splice junction sequences using ensemble transcript annotations. A novoalign v2.08.01 index was created using the combination of the splice junction sequences and zv10 genomic sequence. Reads were aligned to the reference using Novoalign allowing up to 50 alignments for each read. The resulting alignment file was processed with USeq’s SamTranscriptomeParser application which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities. The processed alignments were then run through USeq’s DefinedRegionDifferentialSeq application which counts the number of alignments to each gene Differential expression analysis was generated on the count data with DESeq2 using default settings Genome build: zv10 Supplementary files format and content: Tab delimited text file containing raw counts FPKM values log2FC and FDR values	brain tumor	Normal brain and brain tumors were dissected from zebrafish briefly submerged in RNAlater snap frozen in liquid nitrogen and stored at 80C. To extract RNA samples were thawed and lysed in RLT buffer using Qiagen TissueLyser for 3 min at 25Hz.	Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.	Control and tumor bearing zebrafish were maintained in the animal facility in accordance with Utah Institutional Animal Care and Use Committee.	tissue:brain tumor	GSM2136821	GSM2136821: 9267X8 tumor; Danio rerio; RNA Seq	GSM2136821		1	Total RNA was extracted using Qiagen RNeasy mini kit. Quality of RNA was assessed using Bioanalyzer RNA 6000 Nano Chip and RNA Seq libraries were prepared using Illumnia TruSeq RNA Sapmle Prep v2 with oligo dT kit.	GEO Accession:GSM2136821	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP074122			9267X8_120613_SN141_0510_AC0TF4ACXX_7.txt.gz	fastq	1049619800.0	20992396.0	GSM2136821 r1	0:50	A:284508112;C:243447832;G:236471909;T:285153684;N:38263	50				284508112	243447832	236471909	285153684	38263	SRX1735455	SRS1416508	SRA421168	GEO	Oncological Sciences, University of Utah	1	0.92111		0.10635		0.68061		0.48665		50		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown		United States	2016-04-28	Undetermined	Undetermined	Multi-tissue	Multi-system