run_metadata: 40460

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
40460	SRR3169297	SRX1584898	SRS1302563	SRP070127	PRJNA312107	SATB2 induces transcriptional programs in melanoma that lead to metastatic behavior [RNA Seq]	GSE77922	Transcriptome Analysis	We report gene expression data for zebrafish melanomas overexpressing human SATB2 and EGFP. Overall design: RNA seq was performed on three biological replicates of primary zebrafish melanoma tumors that were excized from MCR:EGFP control and MCR:SATB2 overexpressing TgBRAF V600E;p53 / ; mitf / zebrafish.	parent bioproject:PRJNA312106			MCR:EGFP tumor 2	GSM2061395		source name:EGFP 2\|tissue:primary melanoma tumor\|genotype:Tgmitfa:BRAFV600E; p53 / ; mitfa /	MCR:EGFP tumor 2	Quality control of RNA Seq datasets was performed by FastQC18 and Cutadapt19 to remove adaptor sequences and low quality regions. The high quality reads were aligned to UCSC build danRer7 of zebrafish genome using Tophat20 2.0.11 without xxx splicing form calls. Transcript abundance and differential expression were calculated with Cufflinks21 2.2.1. FPKM values were used to normalize and quantify each transcript. Genome build: Danio rerio UCSC danRer7 Supplementary files format and content: tab delimited text file containg the FPKM value of each gene	EGFP 2	Zebrafish Tgmitfa:BRAFV600E; p53 / ; mitfa / one cell stage embryos were injected with a MiniCoopR expression vector to induce melanocyte specific overexpression of either EGFP control or human SATB2 raised to maturity and monitored for melanoma formation.	Zebrafish melanomas were isolated and mechanically homogenized in RTL buffer Qiagen containing β mercaptoethanol. Tumor lysates were transferred onto a QiaShredder column Qiagen and RNA isolation was performed using the RNA Micro Plus kit Qiagen according to the manufacturers instruction. Total RNA was depleted of ribosomal RNA with the Ribo Zero Gold kit Epicentre. Ribosome depleted RNA was used to create multiplexed RNA seq libraries NEBNext Ultra according to manufacturer's protocol		tissue:primary melanoma tumor\|genotype:Tgmitfa:BRAFV600E; p53 / ; mitfa /	GSM2061395	GSM2061395: MCR:EGFP tumor 2; Danio rerio; RNA Seq	GSM2061395		1	Zebrafish melanomas were isolated and mechanically homogenized in RTL buffer Qiagen containing β mercaptoethanol. Tumor lysates were transferred onto a QiaShredder column Qiagen and RNA isolation was performed using the RNA Micro Plus kit Qiagen according to the manufacturers instruction. Total RNA was depleted of ribosomal RNA with the Ribo Zero Gold kit Epicentre. Ribosome depleted RNA was used to create multiplexed RNA seq libraries NEBNext Ultra according to manufacturer's protocol	GEO Accession:GSM2061395	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP070127			EvR-2_R2.fastq.gz EvR-2_R1.fastq.gz	fastq fastq	7890162016.0	39060208.0	GSM2061395 r1	0:101 1:101	A:2172564285;C:1760424902;G:1758426718;T:2196099270;N:2646841	101	101			2172564285	1760424902	1758426718	2196099270	2646841	SRX1584898	SRS1302563	SRA353730	GEO	Oncology/Hematology, Boston Children's Hospital	2	0.89676	0.89022	0.35914	0.35869	0.72748	0.73328	0.50126	0.48386	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	rrna_depletion	nebnext	bulk	unknown	unknown		United States	2016-02-15	Undetermined	Embryo	Cancer or Tumor	Cancer or Tumor