run_metadata: 51964

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
51964	SRR8928875	SRX5709832	SRS4649003	SRP193005	PRJNA533623	MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease	GSE130037	Transcriptome Analysis	The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.		pubmed:31582381		GC056865 GCGTAGTA TCGACTAG control psbulk	GSM3730586		source name:mitfa:GFP cells from control\|genotype:mitfavc7\|tissue:GFP+ cells from control	GC056865 GCGTAGTA TCGACTAG control psbulk	Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92 20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample	mitfa:GFP cells from control		FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads		genotype:mitfavc7\|tissue:GFP+ cells from control	GSM3730586	GSM3730586: GC056865 GCGTAGTA TCGACTAG control psbulk; Danio rerio; RNA Seq	GSM3730586		1	FACS sorting of 50 GFP+ living cells from control SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730586	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP193005			GC056865_GCGTAGTA-TCGACTAG.R1.fastq.gz GC056865_GCGTAGTA-TCGACTAG.R2.fastq.gz	fastq fastq	397190556.0	1576153.0	GSM3730586 r1	0:126 1:126	A:108614389;C:88489174;G:87744396;T:112305346;N:37251	126	126			108614389	88489174	87744396	112305346	37251	SRX5709832	SRS4649003	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91036	0.90994	0.14864	0.15033	0.82856	0.82775	0.55841	0.55225	126	126	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq		United Kingdom	2019-04-18	Undetermined	Undetermined	Undetermined	Undetermined