metadata: run_metadata: 499 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation

499 rows where experiment.library_selection = "cDNA", technology = "smartseq" and tissue_curation_coarse = "Cancer or Tumor"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	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.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
51886	51886	SRR8928953	SRX5709910	SRS4649081	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	GC056829 TAGCGCTC TCGACTAG primary sc	GSM3730664	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TAGCGCTC TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730664	GSM3730664: GC056829 TAGCGCTC TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730664	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730664	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGCGCTC-TCGACTAG.R1.fastq.gz GC056829_TAGCGCTC-TCGACTAG.R2.fastq.gz	fastq fastq	291297384.0	1155942.0	GSM3730664 r1	0:126 1:126	A:75934677;C:69727236;G:68974546;T:76563463;N:97462	126	126	75934677	69727236	68974546	76563463	97462	SRX5709910	SRS4649081	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91121	0.91015	0.08817	0.08834	0.89858	0.89858	0.51377	0.51817	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	Cancer or Tumor	Cancer or Tumor
51887	51887	SRR8928952	SRX5709909	SRS4649080	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	GC056829 TAGCGCTC CTCTCTAT primary sc	GSM3730663	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TAGCGCTC CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730663	GSM3730663: GC056829 TAGCGCTC CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730663	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730663	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGCGCTC-CTCTCTAT.R1.fastq.gz GC056829_TAGCGCTC-CTCTCTAT.R2.fastq.gz	fastq fastq	113392440.0	449970.0	GSM3730663 r1	0:126 1:126	A:28731494;C:27721828;G:27545627;T:29349373;N:44118	126	126	28731494	27721828	27545627	29349373	44118	SRX5709909	SRS4649080	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.86439	0.8641	0.04586	0.04637	0.96848	0.96828	0.58025	0.58287	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	Cancer or Tumor	Cancer or Tumor
51888	51888	SRR8928951	SRX5709908	SRS4649079	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	GC056829 TAGCGCTC CCTAGAGT primary sc	GSM3730662	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TAGCGCTC CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730662	GSM3730662: GC056829 TAGCGCTC CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730662	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730662	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGCGCTC-CCTAGAGT.R1.fastq.gz GC056829_TAGCGCTC-CCTAGAGT.R2.fastq.gz	fastq fastq	192644172.0	764461.0	GSM3730662 r1	0:126 1:126	A:51220771;C:45349495;G:44426842;T:51583802;N:63262	126	126	51220771	45349495	44426842	51583802	63262	SRX5709908	SRS4649079	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91899	0.91846	0.08338	0.08378	0.9419	0.94205	0.57993	0.58363	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	Cancer or Tumor	Cancer or Tumor
51889	51889	SRR8928950	SRX5709907	SRS4649078	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	GC056829 TAGCGCTC AAGGAGTA regressed sc	GSM3730661	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TAGCGCTC AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730661	GSM3730661: GC056829 TAGCGCTC AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730661	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730661	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGCGCTC-AAGGAGTA.R1.fastq.gz GC056829_TAGCGCTC-AAGGAGTA.R2.fastq.gz	fastq fastq	364945392.0	1448196.0	GSM3730661 r1	0:126 1:126	A:92235356;C:90530535;G:89271040;T:92862459;N:46002	126	126	92235356	90530535	89271040	92862459	46002	SRX5709907	SRS4649078	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89628	0.89675	0.09274	0.09236	0.94817	0.9483	0.54004	0.54001	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	Cancer or Tumor	Cancer or Tumor
51890	51890	SRR8928949	SRX5709906	SRS4649077	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	GC056829 TACGCTGC TCGACTAG primary sc	GSM3730660	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TACGCTGC TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730660	GSM3730660: GC056829 TACGCTGC TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730660	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730660	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-TCGACTAG.R1.fastq.gz GC056829_TACGCTGC-TCGACTAG.R2.fastq.gz	fastq fastq	254888928.0	1011464.0	GSM3730660 r1	0:126 1:126	A:65738264;C:61378795;G:60939053;T:66745851;N:86965	126	126	65738264	61378795	60939053	66745851	86965	SRX5709906	SRS4649077	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.87128	0.87129	0.14421	0.1441	0.94194	0.94136	0.52886	0.52491	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	Cancer or Tumor	Cancer or Tumor
51891	51891	SRR8928948	SRX5709905	SRS4649076	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	GC056829 TACGCTGC GTAAGGAG primary sc	GSM3730659	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TACGCTGC GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730659	GSM3730659: GC056829 TACGCTGC GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730659	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730659	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-GTAAGGAG.R1.fastq.gz GC056829_TACGCTGC-GTAAGGAG.R2.fastq.gz	fastq fastq	178712352.0	709176.0	GSM3730659 r1	0:126 1:126	A:46055648;C:43301884;G:42970793;T:46345442;N:38585	126	126	46055648	43301884	42970793	46345442	38585	SRX5709905	SRS4649076	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.86694	0.86633	0.03958	0.03972	0.95808	0.95826	0.52389	0.52822	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	Cancer or Tumor	Cancer or Tumor
51892	51892	SRR8928947	SRX5709904	SRS4649075	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	GC056829 TACGCTGC GAGCCTTA regressed sc	GSM3730658	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TACGCTGC GAGCCTTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730658	GSM3730658: GC056829 TACGCTGC GAGCCTTA regressed sc; Danio rerio; RNA Seq	GSM3730658	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730658	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-GAGCCTTA.R2.fastq.gz GC056829_TACGCTGC-GAGCCTTA.R1.fastq.gz	fastq fastq	210371868.0	834809.0	GSM3730658 r1	0:126 1:126	A:53815943;C:51360144;G:50821809;T:54331673;N:42299	126	126	53815943	51360144	50821809	54331673	42299	SRX5709904	SRS4649075	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83086	0.83081	0.16142	0.16216	0.95844	0.95893	0.53928	0.54334	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	Cancer or Tumor	Cancer or Tumor
51893	51893	SRR8928946	SRX5709903	SRS4649074	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	GC056829 TACGCTGC CTCTCTAT primary sc	GSM3730657	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TACGCTGC CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730657	GSM3730657: GC056829 TACGCTGC CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730657	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730657	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-CTCTCTAT.R1.fastq.gz GC056829_TACGCTGC-CTCTCTAT.R2.fastq.gz	fastq fastq	267534036.0	1061643.0	GSM3730657 r1	0:126 1:126	A:69417023;C:64596599;G:63565263;T:69859489;N:95662	126	126	69417023	64596599	63565263	69859489	95662	SRX5709903	SRS4649074	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88641	0.88499	0.13392	0.13421	0.92644	0.92598	0.59348	0.58471	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	Cancer or Tumor	Cancer or Tumor
51894	51894	SRR8928945	SRX5709902	SRS4649073	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	GC056829 TACGCTGC CGTCTAAT regressed sc	GSM3730656	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TACGCTGC CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730656	GSM3730656: GC056829 TACGCTGC CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730656	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730656	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-CGTCTAAT.R1.fastq.gz GC056829_TACGCTGC-CGTCTAAT.R2.fastq.gz	fastq fastq	206996328.0	821414.0	GSM3730656 r1	0:126 1:126	A:55682407;C:47711331;G:47331267;T:56217785;N:53538	126	126	55682407	47711331	47331267	56217785	53538	SRX5709902	SRS4649073	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83219	0.83189	0.27024	0.27104	0.94645	0.94617	0.51275	0.51998	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	Cancer or Tumor	Cancer or Tumor
51895	51895	SRR8928944	SRX5709901	SRS4649072	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	GC056829 TACGCTGC CCTAGAGT primary sc	GSM3730655	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TACGCTGC CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730655	GSM3730655: GC056829 TACGCTGC CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730655	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730655	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TACGCTGC-CCTAGAGT.R2.fastq.gz GC056829_TACGCTGC-CCTAGAGT.R1.fastq.gz	fastq fastq	256972212.0	1019731.0	GSM3730655 r1	0:126 1:126	A:66668858;C:61688556;G:60949104;T:67584232;N:81462	126	126	66668858	61688556	60949104	67584232	81462	SRX5709901	SRS4649072	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88856	0.8877	0.12238	0.12328	0.93324	0.93302	0.48855	0.48825	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	Cancer or Tumor	Cancer or Tumor
51896	51896	SRR8928943	SRX5709900	SRS4649071	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	GC056829 TAAGGCGA GTAAGGAG primary sc	GSM3730654	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TAAGGCGA GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730654	GSM3730654: GC056829 TAAGGCGA GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730654	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730654	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAAGGCGA-GTAAGGAG.R1.fastq.gz GC056829_TAAGGCGA-GTAAGGAG.R2.fastq.gz	fastq fastq	260808408.0	1034954.0	GSM3730654 r1	0:126 1:126	A:66411357;C:64521343;G:62517949;T:67296408;N:61351	126	126	66411357	64521343	62517949	67296408	61351	SRX5709900	SRS4649071	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.86131	0.86176	0.04877	0.04898	0.91277	0.91269	0.51465	0.52571	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	Cancer or Tumor	Cancer or Tumor
51897	51897	SRR8928942	SRX5709899	SRS4649070	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	GC056829 TAAGGCGA GAGCCTTA regressed sc	GSM3730653	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TAAGGCGA GAGCCTTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730653	GSM3730653: GC056829 TAAGGCGA GAGCCTTA regressed sc; Danio rerio; RNA Seq	GSM3730653	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730653	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAAGGCGA-GAGCCTTA.R1.fastq.gz GC056829_TAAGGCGA-GAGCCTTA.R2.fastq.gz	fastq fastq	297194436.0	1179343.0	GSM3730653 r1	0:126 1:126	A:75168080;C:73519502;G:72152863;T:76295525;N:58466	126	126	75168080	73519502	72152863	76295525	58466	SRX5709899	SRS4649070	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88378	0.88274	0.10122	0.10215	0.92393	0.9235	0.54285	0.53572	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	Cancer or Tumor	Cancer or Tumor
51898	51898	SRR8928941	SRX5709898	SRS4649069	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	GC056829 TAAGGCGA CGTCTAAT regressed sc	GSM3730652	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TAAGGCGA CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730652	GSM3730652: GC056829 TAAGGCGA CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730652	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730652	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAAGGCGA-CGTCTAAT.R1.fastq.gz GC056829_TAAGGCGA-CGTCTAAT.R2.fastq.gz	fastq fastq	259498260.0	1029755.0	GSM3730652 r1	0:126 1:126	A:67802858;C:61880999;G:61436817;T:68308840;N:68746	126	126	67802858	61880999	61436817	68308840	68746	SRX5709898	SRS4649069	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91807	0.91731	0.06642	0.06685	0.95252	0.95239	0.51124	0.51406	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	Cancer or Tumor	Cancer or Tumor
51899	51899	SRR8928940	SRX5709897	SRS4649068	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	GC056829 TAAGGCGA CCTAGAGT primary sc	GSM3730651	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TAAGGCGA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730651	GSM3730651: GC056829 TAAGGCGA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730651	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730651	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAAGGCGA-CCTAGAGT.R1.fastq.gz GC056829_TAAGGCGA-CCTAGAGT.R2.fastq.gz	fastq fastq	303461676.0	1204213.0	GSM3730651 r1	0:126 1:126	A:79430814;C:73182143;G:71410702;T:79345568;N:92449	126	126	79430814	73182143	71410702	79345568	92449	SRX5709897	SRS4649068	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92438	0.9238	0.06525	0.06568	0.9556	0.95542	0.54114	0.54377	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	Cancer or Tumor	Cancer or Tumor
51900	51900	SRR8928939	SRX5709896	SRS4649067	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	GC056829 GTAGAGGA TCGACTAG primary sc	GSM3730650	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GTAGAGGA TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730650	GSM3730650: GC056829 GTAGAGGA TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730650	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730650	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GTAGAGGA-TCGACTAG.R1.fastq.gz GC056829_GTAGAGGA-TCGACTAG.R2.fastq.gz	fastq fastq	433302408.0	1719454.0	GSM3730650 r1	0:126 1:126	A:110997682;C:105340010;G:105096788;T:111714755;N:153173	126	126	110997682	105340010	105096788	111714755	153173	SRX5709896	SRS4649067	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92247	0.92194	0.07672	0.07664	0.95919	0.95923	0.52868	0.5197	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	Cancer or Tumor	Cancer or Tumor
51901	51901	SRR8928938	SRX5709895	SRS4649066	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	GC056829 GTAGAGGA GAGCCTTA regressed sc	GSM3730649	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GTAGAGGA GAGCCTTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730649	GSM3730649: GC056829 GTAGAGGA GAGCCTTA regressed sc; Danio rerio; RNA Seq	GSM3730649	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730649	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GTAGAGGA-GAGCCTTA.R1.fastq.gz GC056829_GTAGAGGA-GAGCCTTA.R2.fastq.gz	fastq fastq	445825044.0	1769147.0	GSM3730649 r1	0:126 1:126	A:117015733;C:106434668;G:105976952;T:116304639;N:93052	126	126	117015733	106434668	105976952	116304639	93052	SRX5709895	SRS4649066	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83036	0.82993	0.06444	0.06501	0.9722	0.97214	0.50568	0.50383	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	Cancer or Tumor	Cancer or Tumor
51902	51902	SRR8928937	SRX5709894	SRS4649065	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	GC056829 GTAGAGGA CCTAGAGT primary sc	GSM3730648	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GTAGAGGA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730648	GSM3730648: GC056829 GTAGAGGA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730648	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730648	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GTAGAGGA-CCTAGAGT.R1.fastq.gz GC056829_GTAGAGGA-CCTAGAGT.R2.fastq.gz	fastq fastq	397690272.0	1578136.0	GSM3730648 r1	0:126 1:126	A:101261958;C:97297237;G:96894552;T:102107923;N:128602	126	126	101261958	97297237	96894552	102107923	128602	SRX5709894	SRS4649065	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8582	0.85819	0.10612	0.10642	0.97037	0.97033	0.51968	0.5243	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	Cancer or Tumor	Cancer or Tumor
51903	51903	SRR8928936	SRX5709893	SRS4649064	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	GC056829 GGAGCTAC TCGACTAG primary sc	GSM3730647	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGAGCTAC TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730647	GSM3730647: GC056829 GGAGCTAC TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730647	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730647	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGAGCTAC-TCGACTAG.R1.fastq.gz GC056829_GGAGCTAC-TCGACTAG.R2.fastq.gz	fastq fastq	272224260.0	1080255.0	GSM3730647 r1	0:126 1:126	A:70296991;C:65406815;G:65212818;T:71221917;N:85719	126	126	70296991	65406815	65212818	71221917	85719	SRX5709893	SRS4649064	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.90561	0.9043	0.07421	0.07394	0.92358	0.92338	0.51444	0.5232	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	Cancer or Tumor	Cancer or Tumor
51904	51904	SRR8928935	SRX5709892	SRS4649063	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	GC056829 GGAGCTAC GTAAGGAG primary sc	GSM3730646	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGAGCTAC GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730646	GSM3730646: GC056829 GGAGCTAC GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730646	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730646	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGAGCTAC-GTAAGGAG.R2.fastq.gz GC056829_GGAGCTAC-GTAAGGAG.R1.fastq.gz	fastq fastq	287611632.0	1141316.0	GSM3730646 r1	0:126 1:126	A:76256586;C:67883041;G:67401256;T:76016064;N:54685	126	126	76256586	67883041	67401256	76016064	54685	SRX5709892	SRS4649063	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93013	0.93086	0.07017	0.07061	0.91762	0.91774	0.57695	0.57605	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	Cancer or Tumor	Cancer or Tumor
51905	51905	SRR8928934	SRX5709891	SRS4649062	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	GC056829 GGAGCTAC GAGCCTTA regressed sc	GSM3730645	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GGAGCTAC GAGCCTTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730645	GSM3730645: GC056829 GGAGCTAC GAGCCTTA regressed sc; Danio rerio; RNA Seq	GSM3730645	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730645	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGAGCTAC-GAGCCTTA.R1.fastq.gz GC056829_GGAGCTAC-GAGCCTTA.R2.fastq.gz	fastq fastq	464985864.0	1845182.0	GSM3730645 r1	0:126 1:126	A:124575579;C:108881259;G:108095998;T:123334821;N:98207	126	126	124575579	108881259	108095998	123334821	98207	SRX5709891	SRS4649062	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92626	0.92604	0.09489	0.09489	0.96869	0.96806	0.5413	0.53885	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	Cancer or Tumor	Cancer or Tumor
51906	51906	SRR8928933	SRX5709890	SRS4649061	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	GC056829 GGAGCTAC CTCTCTAT primary sc	GSM3730644	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGAGCTAC CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730644	GSM3730644: GC056829 GGAGCTAC CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730644	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730644	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGAGCTAC-CTCTCTAT.R1.fastq.gz GC056829_GGAGCTAC-CTCTCTAT.R2.fastq.gz	fastq fastq	324318708.0	1286979.0	GSM3730644 r1	0:126 1:126	A:86072167;C:76258100;G:75956647;T:85912089;N:119705	126	126	86072167	76258100	75956647	85912089	119705	SRX5709890	SRS4649061	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93143	0.9309	0.06522	0.06492	0.90836	0.90834	0.60667	0.6062	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	Cancer or Tumor	Cancer or Tumor
51907	51907	SRR8928932	SRX5709889	SRS4649060	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	GC056829 GGAGCTAC CCTAGAGT primary sc	GSM3730643	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGAGCTAC CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730643	GSM3730643: GC056829 GGAGCTAC CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730643	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730643	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGAGCTAC-CCTAGAGT.R1.fastq.gz GC056829_GGAGCTAC-CCTAGAGT.R2.fastq.gz	fastq fastq	367668756.0	1459003.0	GSM3730643 r1	0:126 1:126	A:95601300;C:89273573;G:88036913;T:94633240;N:123730	126	126	95601300	89273573	88036913	94633240	123730	SRX5709889	SRS4649060	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93123	0.93045	0.08711	0.08711	0.96771	0.96771	0.53508	0.53992	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	Cancer or Tumor	Cancer or Tumor
51908	51908	SRR8928931	SRX5709888	SRS4649059	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	GC056829 GGACTCCT GTAAGGAG primary sc	GSM3730642	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGACTCCT GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730642	GSM3730642: GC056829 GGACTCCT GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730642	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730642	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGACTCCT-GTAAGGAG.R1.fastq.gz GC056829_GGACTCCT-GTAAGGAG.R2.fastq.gz	fastq fastq	213090948.0	845599.0	GSM3730642 r1	0:126 1:126	A:50960818;C:55323771;G:54367826;T:52395339;N:43194	126	126	50960818	55323771	54367826	52395339	43194	SRX5709888	SRS4649059	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.53616	0.53527	0.32062	0.32031	0.96682	0.96729	0.6416	0.64014	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	Cancer or Tumor	Cancer or Tumor
51909	51909	SRR8928930	SRX5709887	SRS4649058	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	GC056829 GGACTCCT CCTAGAGT primary sc	GSM3730641	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GGACTCCT CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730641	GSM3730641: GC056829 GGACTCCT CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730641	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730641	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGACTCCT-CCTAGAGT.R1.fastq.gz GC056829_GGACTCCT-CCTAGAGT.R2.fastq.gz	fastq fastq	257605488.0	1022244.0	GSM3730641 r1	0:126 1:126	A:68119843;C:60795849;G:59913116;T:68691053;N:85627	126	126	68119843	60795849	59913116	68691053	85627	SRX5709887	SRS4649058	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.87874	0.87734	0.10778	0.10889	0.94032	0.94024	0.53743	0.53908	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	Cancer or Tumor	Cancer or Tumor
51910	51910	SRR8928929	SRX5709886	SRS4649057	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	GC056829 GGACTCCT AAGGAGTA regressed sc	GSM3730640	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GGACTCCT AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730640	GSM3730640: GC056829 GGACTCCT AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730640	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730640	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGACTCCT-AAGGAGTA.R1.fastq.gz GC056829_GGACTCCT-AAGGAGTA.R2.fastq.gz	fastq fastq	410134284.0	1627517.0	GSM3730640 r1	0:126 1:126	A:106764472;C:98752415;G:97507572;T:107061850;N:47975	126	126	106764472	98752415	97507572	107061850	47975	SRX5709886	SRS4649057	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.9482	0.94903	0.07536	0.07527	0.9567	0.95702	0.5165	0.51058	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	Cancer or Tumor	Cancer or Tumor
51911	51911	SRR8928928	SRX5709885	SRS4649056	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	GC056829 GCTCATGA TCGACTAG primary sc	GSM3730639	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GCTCATGA TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730639	GSM3730639: GC056829 GCTCATGA TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730639	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730639	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCTCATGA-TCGACTAG.R1.fastq.gz GC056829_GCTCATGA-TCGACTAG.R2.fastq.gz	fastq fastq	353782044.0	1403897.0	GSM3730639 r1	0:126 1:126	A:87406958;C:89677991;G:87954795;T:88618027;N:124273	126	126	87406958	89677991	87954795	88618027	124273	SRX5709885	SRS4649056	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.64818	0.64806	0.03934	0.03947	0.92973	0.92985	0.52519	0.5294	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	Cancer or Tumor	Cancer or Tumor
51912	51912	SRR8928927	SRX5709884	SRS4649055	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	GC056829 GCTCATGA CTATTAAG regressed sc	GSM3730638	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GCTCATGA CTATTAAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730638	GSM3730638: GC056829 GCTCATGA CTATTAAG regressed sc; Danio rerio; RNA Seq	GSM3730638	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730638	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCTCATGA-CTATTAAG.R1.fastq.gz GC056829_GCTCATGA-CTATTAAG.R2.fastq.gz	fastq fastq	174987036.0	694393.0	GSM3730638 r1	0:126 1:126	A:44562605;C:42701764;G:42380021;T:45297509;N:45137	126	126	44562605	42701764	42380021	45297509	45137	SRX5709884	SRS4649055	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.75262	0.74983	0.0668	0.06662	0.97755	0.9777	0.56945	0.6091	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	Cancer or Tumor	Cancer or Tumor
51913	51913	SRR8928926	SRX5709883	SRS4649054	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	GC056829 GCTCATGA CGTCTAAT regressed sc	GSM3730637	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GCTCATGA CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730637	GSM3730637: GC056829 GCTCATGA CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730637	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730637	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCTCATGA-CGTCTAAT.R2.fastq.gz GC056829_GCTCATGA-CGTCTAAT.R1.fastq.gz	fastq fastq	287517132.0	1140941.0	GSM3730637 r1	0:126 1:126	A:71145741;C:72949003;G:71271413;T:72064169;N:86806	126	126	71145741	72949003	71271413	72064169	86806	SRX5709883	SRS4649054	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.64938	0.64843	0.15917	0.15976	0.96818	0.96822	0.49891	0.50203	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	Cancer or Tumor	Cancer or Tumor
51914	51914	SRR8928925	SRX5709882	SRS4649053	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	GC056829 GCTCATGA CCTAGAGT primary sc	GSM3730636	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GCTCATGA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730636	GSM3730636: GC056829 GCTCATGA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730636	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730636	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCTCATGA-CCTAGAGT.R1.fastq.gz GC056829_GCTCATGA-CCTAGAGT.R2.fastq.gz	fastq fastq	370336932.0	1469591.0	GSM3730636 r1	0:126 1:126	A:96296167;C:89074432;G:88213690;T:96631166;N:121477	126	126	96296167	89074432	88213690	96631166	121477	SRX5709882	SRS4649053	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93156	0.93124	0.05341	0.05392	0.92748	0.92697	0.49899	0.50392	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	Cancer or Tumor	Cancer or Tumor
51915	51915	SRR8928924	SRX5709881	SRS4649052	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	GC056829 GCTCATGA AAGGAGTA regressed sc	GSM3730635	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GCTCATGA AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730635	GSM3730635: GC056829 GCTCATGA AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730635	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730635	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCTCATGA-AAGGAGTA.R2.fastq.gz GC056829_GCTCATGA-AAGGAGTA.R1.fastq.gz	fastq fastq	190151640.0	754570.0	GSM3730635 r1	0:126 1:126	A:49341121;C:45650863;G:45201975;T:49935511;N:22170	126	126	49341121	45650863	45201975	49935511	22170	SRX5709881	SRS4649052	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.82617	0.82504	0.12406	0.12366	0.96366	0.96325	0.52592	0.52295	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	Cancer or Tumor	Cancer or Tumor
51916	51916	SRR8928923	SRX5709880	SRS4649051	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	GC056829 GCGTAGTA GTAAGGAG primary sc	GSM3730634	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GCGTAGTA GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730634	GSM3730634: GC056829 GCGTAGTA GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730634	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730634	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCGTAGTA-GTAAGGAG.R1.fastq.gz GC056829_GCGTAGTA-GTAAGGAG.R2.fastq.gz	fastq fastq	317661876.0	1260563.0	GSM3730634 r1	0:126 1:126	A:80432393;C:78414349;G:77436698;T:81297630;N:80806	126	126	80432393	78414349	77436698	81297630	80806	SRX5709880	SRS4649051	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92826	0.92949	0.02341	0.0233	0.95379	0.95379	0.59249	0.58221	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	Cancer or Tumor	Cancer or Tumor
51917	51917	SRR8928922	SRX5709879	SRS4649050	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	GC056829 GCGTAGTA CTCTCTAT primary sc	GSM3730633	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GCGTAGTA CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730633	GSM3730633: GC056829 GCGTAGTA CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730633	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730633	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCGTAGTA-CTCTCTAT.R1.fastq.gz GC056829_GCGTAGTA-CTCTCTAT.R2.fastq.gz	fastq fastq	193812696.0	769098.0	GSM3730633 r1	0:126 1:126	A:48814131;C:47998444;G:47535739;T:49387687;N:76695	126	126	48814131	47998444	47535739	49387687	76695	SRX5709879	SRS4649050	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.80328	0.80016	0.06616	0.06613	0.97542	0.97579	0.5603	0.55613	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	Cancer or Tumor	Cancer or Tumor
51918	51918	SRR8928921	SRX5709878	SRS4649049	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	GC056829 GCGTAGTA CGTCTAAT regressed sc	GSM3730632	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GCGTAGTA CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730632	GSM3730632: GC056829 GCGTAGTA CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730632	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730632	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCGTAGTA-CGTCTAAT.R1.fastq.gz GC056829_GCGTAGTA-CGTCTAAT.R2.fastq.gz	fastq fastq	267262884.0	1060567.0	GSM3730632 r1	0:126 1:126	A:76013138;C:57541943;G:56703402;T:76905939;N:98462	126	126	76013138	57541943	56703402	76905939	98462	SRX5709878	SRS4649049	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.82152	0.82101	0.65549	0.6553	0.84293	0.84488	0.47593	0.47841	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	Cancer or Tumor	Cancer or Tumor
51919	51919	SRR8928920	SRX5709877	SRS4649048	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	GC056829 GCGTAGTA CCTAGAGT primary sc	GSM3730631	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 GCGTAGTA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730631	GSM3730631: GC056829 GCGTAGTA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730631	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730631	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCGTAGTA-CCTAGAGT.R1.fastq.gz GC056829_GCGTAGTA-CCTAGAGT.R2.fastq.gz	fastq fastq	295775676.0	1173713.0	GSM3730631 r1	0:126 1:126	A:76963138;C:70770686;G:70450608;T:77489787;N:101457	126	126	76963138	70770686	70450608	77489787	101457	SRX5709877	SRS4649048	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.94687	0.94561	0.06761	0.06788	0.94754	0.94746	0.54524	0.54217	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	Cancer or Tumor	Cancer or Tumor
51920	51920	SRR8928919	SRX5709876	SRS4649047	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	GC056829 GCGTAGTA AAGGAGTA regressed sc	GSM3730630	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 GCGTAGTA AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730630	GSM3730630: GC056829 GCGTAGTA AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730630	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730630	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GCGTAGTA-AAGGAGTA.R1.fastq.gz GC056829_GCGTAGTA-AAGGAGTA.R2.fastq.gz	fastq fastq	266291172.0	1056711.0	GSM3730630 r1	0:126 1:126	A:67299612;C:66104549;G:64907698;T:67942190;N:37123	126	126	67299612	66104549	64907698	67942190	37123	SRX5709876	SRS4649047	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8119	0.80977	0.10658	0.10635	0.97619	0.97619	0.51591	0.51594	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	Cancer or Tumor	Cancer or Tumor
51921	51921	SRR8928918	SRX5709875	SRS4649046	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	GC056829 CTCTCTAC TCGACTAG primary sc	GSM3730629	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CTCTCTAC TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730629	GSM3730629: GC056829 CTCTCTAC TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730629	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730629	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CTCTCTAC-TCGACTAG.R1.fastq.gz GC056829_CTCTCTAC-TCGACTAG.R2.fastq.gz	fastq fastq	260669556.0	1034403.0	GSM3730629 r1	0:126 1:126	A:65943060;C:64309373;G:63416155;T:66919090;N:81878	126	126	65943060	64309373	63416155	66919090	81878	SRX5709875	SRS4649046	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.82058	0.81768	0.11816	0.11783	0.95883	0.95925	0.51253	0.52836	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	Cancer or Tumor	Cancer or Tumor
51922	51922	SRR8928917	SRX5709874	SRS4649045	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	GC056829 CTCTCTAC GTAAGGAG primary sc	GSM3730628	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CTCTCTAC GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730628	GSM3730628: GC056829 CTCTCTAC GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730628	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730628	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CTCTCTAC-GTAAGGAG.R1.fastq.gz GC056829_CTCTCTAC-GTAAGGAG.R2.fastq.gz	fastq fastq	354950820.0	1408535.0	GSM3730628 r1	0:126 1:126	A:90534360;C:87205898;G:85412817;T:91720134;N:77611	126	126	90534360	87205898	85412817	91720134	77611	SRX5709874	SRS4649045	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.921	0.92101	0.07632	0.07647	0.91741	0.91727	0.54013	0.5449	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	Cancer or Tumor	Cancer or Tumor
51923	51923	SRR8928916	SRX5709873	SRS4649044	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	GC056829 CTCTCTAC CTATTAAG regressed sc	GSM3730627	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 CTCTCTAC CTATTAAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730627	GSM3730627: GC056829 CTCTCTAC CTATTAAG regressed sc; Danio rerio; RNA Seq	GSM3730627	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730627	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CTCTCTAC-CTATTAAG.R1.fastq.gz GC056829_CTCTCTAC-CTATTAAG.R2.fastq.gz	fastq fastq	368561088.0	1462544.0	GSM3730627 r1	0:126 1:126	A:96784754;C:87751359;G:85751825;T:98169508;N:103642	126	126	96784754	87751359	85751825	98169508	103642	SRX5709873	SRS4649044	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.90922	0.90938	0.12334	0.12384	0.97344	0.97378	0.51103	0.51391	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	Cancer or Tumor	Cancer or Tumor
51924	51924	SRR8928915	SRX5709872	SRS4649043	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	GC056829 CTCTCTAC CCTAGAGT primary sc	GSM3730626	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CTCTCTAC CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730626	GSM3730626: GC056829 CTCTCTAC CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730626	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730626	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CTCTCTAC-CCTAGAGT.R1.fastq.gz GC056829_CTCTCTAC-CCTAGAGT.R2.fastq.gz	fastq fastq	228581136.0	907068.0	GSM3730626 r1	0:126 1:126	A:58970927;C:55228424;G:54533564;T:59772230;N:75991	126	126	58970927	55228424	54533564	59772230	75991	SRX5709872	SRS4649043	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.85255	0.85056	0.14666	0.14552	0.95367	0.95394	0.51509	0.50643	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	Cancer or Tumor	Cancer or Tumor
51925	51925	SRR8928914	SRX5709871	SRS4649042	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	GC056829 CGTACTAG GTAAGGAG primary sc	GSM3730625	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGTACTAG GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730625	GSM3730625: GC056829 CGTACTAG GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730625	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730625	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGTACTAG-GTAAGGAG.R2.fastq.gz GC056829_CGTACTAG-GTAAGGAG.R1.fastq.gz	fastq fastq	292363596.0	1160173.0	GSM3730625 r1	0:126 1:126	A:78720402;C:67491387;G:67193252;T:78887746;N:70809	126	126	78720402	67491387	67193252	78887746	70809	SRX5709871	SRS4649042	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.82931	0.83014	0.11384	0.11498	0.96126	0.96159	0.6044	0.60693	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	Cancer or Tumor	Cancer or Tumor
51926	51926	SRR8928913	SRX5709870	SRS4649041	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	GC056829 CGTACTAG CCTAGAGT primary sc	GSM3730624	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGTACTAG CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730624	GSM3730624: GC056829 CGTACTAG CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730624	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730624	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGTACTAG-CCTAGAGT.R1.fastq.gz GC056829_CGTACTAG-CCTAGAGT.R2.fastq.gz	fastq fastq	434637756.0	1724753.0	GSM3730624 r1	0:126 1:126	A:113940379;C:104035935;G:103328127;T:113181597;N:151718	126	126	113940379	104035935	103328127	113181597	151718	SRX5709870	SRS4649041	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.95175	0.95215	0.06962	0.07021	0.96757	0.96777	0.53557	0.51065	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	Cancer or Tumor	Cancer or Tumor
51927	51927	SRR8928912	SRX5709869	SRS4649040	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	GC056829 CGGAGCCT TCGACTAG primary sc	GSM3730623	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGGAGCCT TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730623	GSM3730623: GC056829 CGGAGCCT TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730623	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730623	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGGAGCCT-TCGACTAG.R2.fastq.gz GC056829_CGGAGCCT-TCGACTAG.R1.fastq.gz	fastq fastq	302281056.0	1199528.0	GSM3730623 r1	0:126 1:126	A:76982582;C:74122628;G:73560916;T:77515354;N:99576	126	126	76982582	74122628	73560916	77515354	99576	SRX5709869	SRS4649040	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.9223	0.9222	0.12025	0.12134	0.9335	0.93336	0.55835	0.55812	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	Cancer or Tumor	Cancer or Tumor
51928	51928	SRR8928911	SRX5709868	SRS4649039	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	GC056829 CGGAGCCT GTAAGGAG primary sc	GSM3730622	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGGAGCCT GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730622	GSM3730622: GC056829 CGGAGCCT GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730622	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730622	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGGAGCCT-GTAAGGAG.R1.fastq.gz GC056829_CGGAGCCT-GTAAGGAG.R2.fastq.gz	fastq fastq	379878912.0	1507456.0	GSM3730622 r1	0:126 1:126	A:99469342;C:90368021;G:90380840;T:99582923;N:77786	126	126	99469342	90368021	90380840	99582923	77786	SRX5709868	SRS4649039	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92343	0.92378	0.01303	0.01312	0.96692	0.96704	0.66731	0.66197	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	Cancer or Tumor	Cancer or Tumor
51929	51929	SRR8928910	SRX5709867	SRS4649038	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	GC056829 CGGAGCCT CTCTCTAT primary sc	GSM3730621	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGGAGCCT CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730621	GSM3730621: GC056829 CGGAGCCT CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730621	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730621	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGGAGCCT-CTCTCTAT.R1.fastq.gz GC056829_CGGAGCCT-CTCTCTAT.R2.fastq.gz	fastq fastq	380707992.0	1510746.0	GSM3730621 r1	0:126 1:126	A:100492231;C:89160366;G:89342461;T:101572490;N:140444	126	126	100492231	89160366	89342461	101572490	140444	SRX5709867	SRS4649038	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89447	0.89462	0.08758	0.08783	0.96029	0.96073	0.61664	0.61145	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	Cancer or Tumor	Cancer or Tumor
51930	51930	SRR8928909	SRX5709866	SRS4649037	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	GC056829 CGGAGCCT CCTAGAGT primary sc	GSM3730620	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGGAGCCT CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730620	GSM3730620: GC056829 CGGAGCCT CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730620	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730620	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGGAGCCT-CCTAGAGT.R1.fastq.gz GC056829_CGGAGCCT-CCTAGAGT.R2.fastq.gz	fastq fastq	312036984.0	1238242.0	GSM3730620 r1	0:126 1:126	A:82414080;C:74048144;G:73601241;T:81870053;N:103466	126	126	82414080	74048144	73601241	81870053	103466	SRX5709866	SRS4649037	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93865	0.93885	0.104	0.10381	0.93192	0.93172	0.51626	0.52179	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	Cancer or Tumor	Cancer or Tumor
51931	51931	SRR8928908	SRX5709865	SRS4649036	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	GC056829 CGGAGCCT AAGGAGTA regressed sc	GSM3730619	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 CGGAGCCT AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730619	GSM3730619: GC056829 CGGAGCCT AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730619	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730619	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGGAGCCT-AAGGAGTA.R1.fastq.gz GC056829_CGGAGCCT-AAGGAGTA.R2.fastq.gz	fastq fastq	465135300.0	1845775.0	GSM3730619 r1	0:126 1:126	A:120560965;C:112616285;G:112033016;T:119873868;N:51166	126	126	120560965	112616285	112033016	119873868	51166	SRX5709865	SRS4649036	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.87935	0.87844	0.07001	0.07	0.96463	0.96487	0.48605	0.49489	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	Cancer or Tumor	Cancer or Tumor
51932	51932	SRR8928907	SRX5709864	SRS4649035	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	GC056829 CGATCAGT TCGACTAG primary sc	GSM3730618	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGATCAGT TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730618	GSM3730618: GC056829 CGATCAGT TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730618	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730618	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGATCAGT-TCGACTAG.R2.fastq.gz GC056829_CGATCAGT-TCGACTAG.R1.fastq.gz	fastq fastq	401671620.0	1593935.0	GSM3730618 r1	0:126 1:126	A:107942066;C:93832903;G:93093842;T:106664240;N:138569	126	126	107942066	93832903	93093842	106664240	138569	SRX5709864	SRS4649035	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.94282	0.94328	0.09875	0.09926	0.95205	0.95278	0.55849	0.56528	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	Cancer or Tumor	Cancer or Tumor
51933	51933	SRR8928906	SRX5709863	SRS4649034	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	GC056829 CGATCAGT CTATTAAG regressed sc	GSM3730617	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 CGATCAGT CTATTAAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730617	GSM3730617: GC056829 CGATCAGT CTATTAAG regressed sc; Danio rerio; RNA Seq	GSM3730617	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730617	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGATCAGT-CTATTAAG.R1.fastq.gz GC056829_CGATCAGT-CTATTAAG.R2.fastq.gz	fastq fastq	379605492.0	1506371.0	GSM3730617 r1	0:126 1:126	A:101635072;C:88354828;G:88181651;T:101329817;N:104124	126	126	101635072	88354828	88181651	101329817	104124	SRX5709863	SRS4649034	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.86399	0.86303	0.10358	0.10353	0.96319	0.96276	0.55959	0.56244	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	Cancer or Tumor	Cancer or Tumor
51934	51934	SRR8928905	SRX5709862	SRS4649033	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	GC056829 CGATCAGT CCTAGAGT primary sc	GSM3730616	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGATCAGT CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730616	GSM3730616: GC056829 CGATCAGT CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730616	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730616	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGATCAGT-CCTAGAGT.R1.fastq.gz GC056829_CGATCAGT-CCTAGAGT.R2.fastq.gz	fastq fastq	340445448.0	1350974.0	GSM3730616 r1	0:126 1:126	A:86771809;C:83519567;G:82756237;T:87281566;N:116269	126	126	86771809	83519567	82756237	87281566	116269	SRX5709862	SRS4649033	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89228	0.89189	0.10776	0.10796	0.96402	0.964	0.47821	0.48268	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	Cancer or Tumor	Cancer or Tumor
51935	51935	SRR8928904	SRX5709861	SRS4649032	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	GC056829 CGAGGCTG TCGACTAG primary sc	GSM3730615	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGAGGCTG TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730615	GSM3730615: GC056829 CGAGGCTG TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730615	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730615	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGAGGCTG-TCGACTAG.R1.fastq.gz GC056829_CGAGGCTG-TCGACTAG.R2.fastq.gz	fastq fastq	476092008.0	1889254.0	GSM3730615 r1	0:126 1:126	A:128028428;C:111389746;G:110145876;T:126351414;N:176544	126	126	128028428	111389746	110145876	126351414	176544	SRX5709861	SRS4649032	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93199	0.93201	0.11154	0.11214	0.96536	0.9656	0.52588	0.52971	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	Cancer or Tumor	Cancer or Tumor
51936	51936	SRR8928903	SRX5709860	SRS4649031	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	GC056829 CGAGGCTG CTCTCTAT primary sc	GSM3730614	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGAGGCTG CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730614	GSM3730614: GC056829 CGAGGCTG CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730614	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730614	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGAGGCTG-CTCTCTAT.R2.fastq.gz GC056829_CGAGGCTG-CTCTCTAT.R1.fastq.gz	fastq fastq	256406724.0	1017487.0	GSM3730614 r1	0:126 1:126	A:71824445;C:56378237;G:55961856;T:72137461;N:104725	126	126	71824445	56378237	55961856	72137461	104725	SRX5709860	SRS4649031	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89644	0.89644	0.1951	0.19541	0.9559	0.95613	0.5796	0.57535	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	Cancer or Tumor	Cancer or Tumor
51937	51937	SRR8928902	SRX5709859	SRS4649030	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	GC056829 CGAGGCTG CCTAGAGT primary sc	GSM3730613	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CGAGGCTG CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730613	GSM3730613: GC056829 CGAGGCTG CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730613	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730613	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CGAGGCTG-CCTAGAGT.R1.fastq.gz GC056829_CGAGGCTG-CCTAGAGT.R2.fastq.gz	fastq fastq	311507532.0	1236141.0	GSM3730613 r1	0:126 1:126	A:81033955;C:74697069;G:74271220;T:81398146;N:107142	126	126	81033955	74697069	74271220	81398146	107142	SRX5709859	SRS4649030	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92219	0.92334	0.09021	0.09101	0.95592	0.95639	0.53754	0.54476	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	Cancer or Tumor	Cancer or Tumor
51938	51938	SRR8928901	SRX5709858	SRS4649029	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	GC056829 CCTAAGAC TCGACTAG primary sc	GSM3730612	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CCTAAGAC TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730612	GSM3730612: GC056829 CCTAAGAC TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730612	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730612	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CCTAAGAC-TCGACTAG.R1.fastq.gz GC056829_CCTAAGAC-TCGACTAG.R2.fastq.gz	fastq fastq	184644180.0	732715.0	GSM3730612 r1	0:126 1:126	A:47300051;C:44830087;G:44439723;T:48005022;N:69297	126	126	47300051	44830087	44439723	48005022	69297	SRX5709858	SRS4649029	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8914	0.88957	0.06429	0.06418	0.95252	0.95219	0.50768	0.51797	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	Cancer or Tumor	Cancer or Tumor
51939	51939	SRR8928900	SRX5709857	SRS4649028	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	GC056829 CCTAAGAC CTCTCTAT primary sc	GSM3730611	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 CCTAAGAC CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730611	GSM3730611: GC056829 CCTAAGAC CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730611	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730611	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CCTAAGAC-CTCTCTAT.R1.fastq.gz GC056829_CCTAAGAC-CTCTCTAT.R2.fastq.gz	fastq fastq	116781588.0	463419.0	GSM3730611 r1	0:126 1:126	A:30352318;C:27948316;G:27661468;T:30782768;N:36718	126	126	30352318	27948316	27661468	30782768	36718	SRX5709857	SRS4649028	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.85153	0.8504	0.12109	0.12079	0.95367	0.95335	0.51703	0.55886	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	Cancer or Tumor	Cancer or Tumor
51940	51940	SRR8928899	SRX5709856	SRS4649027	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	GC056829 CCTAAGAC AAGGAGTA regressed sc	GSM3730610	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 CCTAAGAC AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730610	GSM3730610: GC056829 CCTAAGAC AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730610	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730610	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_CCTAAGAC-AAGGAGTA.R1.fastq.gz GC056829_CCTAAGAC-AAGGAGTA.R2.fastq.gz	fastq fastq	244965168.0	972084.0	GSM3730610 r1	0:126 1:126	A:62671882;C:60289717;G:58412757;T:63547681;N:43131	126	126	62671882	60289717	58412757	63547681	43131	SRX5709856	SRS4649027	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91661	0.91524	0.0573	0.05765	0.93048	0.93074	0.52077	0.52291	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	Cancer or Tumor	Cancer or Tumor
51941	51941	SRR8928898	SRX5709855	SRS4649026	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	GC056829 ATGCGCAG TCGACTAG primary sc	GSM3730609	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ATGCGCAG TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730609	GSM3730609: GC056829 ATGCGCAG TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730609	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730609	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATGCGCAG-TCGACTAG.R1.fastq.gz GC056829_ATGCGCAG-TCGACTAG.R2.fastq.gz	fastq fastq	282727872.0	1121936.0	GSM3730609 r1	0:126 1:126	A:74464844;C:68230118;G:66090423;T:73842477;N:100010	126	126	74464844	68230118	66090423	73842477	100010	SRX5709855	SRS4649026	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92501	0.92304	0.04471	0.04503	0.91885	0.9193	0.62994	0.63107	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	Cancer or Tumor	Cancer or Tumor
51942	51942	SRR8928897	SRX5709854	SRS4649025	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	GC056829 ATGCGCAG GAGCCTTA regressed sc	GSM3730608	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ATGCGCAG GAGCCTTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730608	GSM3730608: GC056829 ATGCGCAG GAGCCTTA regressed sc; Danio rerio; RNA Seq	GSM3730608	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730608	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATGCGCAG-GAGCCTTA.R1.fastq.gz GC056829_ATGCGCAG-GAGCCTTA.R2.fastq.gz	fastq fastq	358866144.0	1424072.0	GSM3730608 r1	0:126 1:126	A:97607473;C:81909382;G:81595961;T:97683192;N:70136	126	126	97607473	81909382	81595961	97683192	70136	SRX5709854	SRS4649025	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.82323	0.82462	0.35241	0.35457	0.96244	0.96238	0.55819	0.55426	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	Cancer or Tumor	Cancer or Tumor
51943	51943	SRR8928896	SRX5709853	SRS4649024	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	GC056829 ATGCGCAG CTATTAAG regressed sc	GSM3730607	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ATGCGCAG CTATTAAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730607	GSM3730607: GC056829 ATGCGCAG CTATTAAG regressed sc; Danio rerio; RNA Seq	GSM3730607	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730607	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATGCGCAG-CTATTAAG.R1.fastq.gz GC056829_ATGCGCAG-CTATTAAG.R2.fastq.gz	fastq fastq	244324584.0	969542.0	GSM3730607 r1	0:126 1:126	A:65140140;C:57191901;G:57082577;T:64848961;N:61005	126	126	65140140	57191901	57082577	64848961	61005	SRX5709853	SRS4649024	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92726	0.92704	0.07588	0.07551	0.95217	0.95237	0.53228	0.54088	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	Cancer or Tumor	Cancer or Tumor
51944	51944	SRR8928895	SRX5709852	SRS4649023	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	GC056829 ATGCGCAG CCTAGAGT primary sc	GSM3730606	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ATGCGCAG CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730606	GSM3730606: GC056829 ATGCGCAG CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730606	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730606	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATGCGCAG-CCTAGAGT.R1.fastq.gz GC056829_ATGCGCAG-CCTAGAGT.R2.fastq.gz	fastq fastq	307891584.0	1221792.0	GSM3730606 r1	0:126 1:126	A:82078706;C:72584581;G:71698098;T:81431988;N:98211	126	126	82078706	72584581	71698098	81431988	98211	SRX5709852	SRS4649023	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91708	0.91724	0.10959	0.10962	0.9362	0.93661	0.57872	0.58025	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	Cancer or Tumor	Cancer or Tumor
51945	51945	SRR8928894	SRX5709851	SRS4649022	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	GC056829 ATGCGCAG AAGGAGTA regressed sc	GSM3730605	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ATGCGCAG AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730605	GSM3730605: GC056829 ATGCGCAG AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730605	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730605	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATGCGCAG-AAGGAGTA.R1.fastq.gz GC056829_ATGCGCAG-AAGGAGTA.R2.fastq.gz	fastq fastq	275463972.0	1093111.0	GSM3730605 r1	0:126 1:126	A:75741901;C:62501937;G:61994880;T:75190726;N:34528	126	126	75741901	62501937	61994880	75190726	34528	SRX5709851	SRS4649022	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93257	0.93274	0.15094	0.15237	0.95408	0.95438	0.51652	0.51548	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	Cancer or Tumor	Cancer or Tumor
51946	51946	SRR8928893	SRX5709850	SRS4649021	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	GC056829 ATCTCAGG TCGACTAG primary sc	GSM3730604	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ATCTCAGG TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730604	GSM3730604: GC056829 ATCTCAGG TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730604	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730604	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATCTCAGG-TCGACTAG.R1.fastq.gz GC056829_ATCTCAGG-TCGACTAG.R2.fastq.gz	fastq fastq	327675348.0	1300299.0	GSM3730604 r1	0:126 1:126	A:86866448;C:77421254;G:76718936;T:86551535;N:117175	126	126	86866448	77421254	76718936	86551535	117175	SRX5709850	SRS4649021	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92954	0.92863	0.07841	0.0784	0.94349	0.94343	0.53765	0.5388	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	Cancer or Tumor	Cancer or Tumor
51947	51947	SRR8928892	SRX5709849	SRS4649020	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	GC056829 ATCTCAGG GTAAGGAG primary sc	GSM3730603	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ATCTCAGG GTAAGGAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730603	GSM3730603: GC056829 ATCTCAGG GTAAGGAG primary sc; Danio rerio; RNA Seq	GSM3730603	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730603	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATCTCAGG-GTAAGGAG.R1.fastq.gz GC056829_ATCTCAGG-GTAAGGAG.R2.fastq.gz	fastq fastq	282332484.0	1120367.0	GSM3730603 r1	0:126 1:126	A:76000840;C:65857715;G:65028482;T:75387976;N:57471	126	126	76000840	65857715	65028482	75387976	57471	SRX5709849	SRS4649020	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.9242	0.92428	0.09622	0.0967	0.93385	0.93403	0.52269	0.53263	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	Cancer or Tumor	Cancer or Tumor
51948	51948	SRR8928891	SRX5709848	SRS4649019	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	GC056829 ATCTCAGG CCTAGAGT primary sc	GSM3730602	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ATCTCAGG CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730602	GSM3730602: GC056829 ATCTCAGG CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730602	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730602	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ATCTCAGG-CCTAGAGT.R1.fastq.gz GC056829_ATCTCAGG-CCTAGAGT.R2.fastq.gz	fastq fastq	407470644.0	1616947.0	GSM3730602 r1	0:126 1:126	A:107092339;C:96989033;G:96203618;T:107058284;N:127370	126	126	107092339	96989033	96203618	107058284	127370	SRX5709848	SRS4649019	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89269	0.89242	0.10256	0.10329	0.96692	0.96712	0.46786	0.47313	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	Cancer or Tumor	Cancer or Tumor
51949	51949	SRR8928890	SRX5709847	SRS4649018	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	GC056829 AGGCAGAA CCTAGAGT primary sc	GSM3730601	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 AGGCAGAA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730601	GSM3730601: GC056829 AGGCAGAA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730601	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730601	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AGGCAGAA-CCTAGAGT.R1.fastq.gz GC056829_AGGCAGAA-CCTAGAGT.R2.fastq.gz	fastq fastq	293820156.0	1165953.0	GSM3730601 r1	0:126 1:126	A:76372543;C:70822823;G:69612395;T:76918743;N:93652	126	126	76372543	70822823	69612395	76918743	93652	SRX5709847	SRS4649018	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88851	0.88731	0.06948	0.06976	0.9347	0.93488	0.54933	0.54671	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	Cancer or Tumor	Cancer or Tumor
51950	51950	SRR8928889	SRX5709846	SRS4649017	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	GC056829 ACTGAGCG TCGACTAG primary sc	GSM3730600	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ACTGAGCG TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730600	GSM3730600: GC056829 ACTGAGCG TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730600	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730600	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTGAGCG-TCGACTAG.R1.fastq.gz GC056829_ACTGAGCG-TCGACTAG.R2.fastq.gz	fastq fastq	500221764.0	1985007.0	GSM3730600 r1	0:126 1:126	A:131583276;C:118757665;G:118489181;T:131215901;N:175741	126	126	131583276	118757665	118489181	131215901	175741	SRX5709846	SRS4649017	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.94418	0.9442	0.0933	0.09315	0.96012	0.95972	0.50888	0.51235	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	Cancer or Tumor	Cancer or Tumor
51951	51951	SRR8928888	SRX5709845	SRS4649016	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	GC056829 ACTGAGCG CTATTAAG regressed sc	GSM3730599	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ACTGAGCG CTATTAAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730599	GSM3730599: GC056829 ACTGAGCG CTATTAAG regressed sc; Danio rerio; RNA Seq	GSM3730599	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730599	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTGAGCG-CTATTAAG.R2.fastq.gz GC056829_ACTGAGCG-CTATTAAG.R1.fastq.gz	fastq fastq	207892692.0	824971.0	GSM3730599 r1	0:126 1:126	A:56712227;C:47294339;G:47261688;T:56567223;N:57215	126	126	56712227	47294339	47261688	56567223	57215	SRX5709845	SRS4649016	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8994	0.89987	0.17767	0.17946	0.92129	0.92096	0.53379	0.54233	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	Cancer or Tumor	Cancer or Tumor
51952	51952	SRR8928887	SRX5709844	SRS4649015	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	GC056829 ACTGAGCG CCTAGAGT primary sc	GSM3730598	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ACTGAGCG CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730598	GSM3730598: GC056829 ACTGAGCG CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730598	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730598	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTGAGCG-CCTAGAGT.R2.fastq.gz GC056829_ACTGAGCG-CCTAGAGT.R1.fastq.gz	fastq fastq	295774416.0	1173708.0	GSM3730598 r1	0:126 1:126	A:77069169;C:71304130;G:70621480;T:76681089;N:98548	126	126	77069169	71304130	70621480	76681089	98548	SRX5709844	SRS4649015	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92661	0.92506	0.07486	0.07512	0.93294	0.93322	0.54126	0.54517	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	Cancer or Tumor	Cancer or Tumor
51953	51953	SRR8928886	SRX5709843	SRS4649014	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	GC056829 ACTGAGCG AAGGAGTA regressed sc	GSM3730597	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ACTGAGCG AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730597	GSM3730597: GC056829 ACTGAGCG AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730597	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730597	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTGAGCG-AAGGAGTA.R2.fastq.gz GC056829_ACTGAGCG-AAGGAGTA.R1.fastq.gz	fastq fastq	278612460.0	1105605.0	GSM3730597 r1	0:126 1:126	A:75613297;C:64058449;G:63787377;T:75106998;N:46339	126	126	75613297	64058449	63787377	75106998	46339	SRX5709843	SRS4649014	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.86689	0.86623	0.12841	0.12974	0.97238	0.97246	0.53458	0.54091	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	Cancer or Tumor	Cancer or Tumor
51954	51954	SRR8928885	SRX5709842	SRS4649013	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	GC056829 ACTCGCTA TCGACTAG primary sc	GSM3730596	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ACTCGCTA TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730596	GSM3730596: GC056829 ACTCGCTA TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730596	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730596	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTCGCTA-TCGACTAG.R1.fastq.gz GC056829_ACTCGCTA-TCGACTAG.R2.fastq.gz	fastq fastq	313971084.0	1245917.0	GSM3730596 r1	0:126 1:126	A:80216833;C:76648971;G:75871740;T:81139748;N:93792	126	126	80216833	76648971	75871740	81139748	93792	SRX5709842	SRS4649013	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92707	0.92661	0.05317	0.05333	0.93701	0.93657	0.51638	0.5206	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	Cancer or Tumor	Cancer or Tumor
51955	51955	SRR8928884	SRX5709841	SRS4649012	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	GC056829 ACTCGCTA CGTCTAAT regressed sc	GSM3730595	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 ACTCGCTA CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730595	GSM3730595: GC056829 ACTCGCTA CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730595	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730595	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTCGCTA-CGTCTAAT.R1.fastq.gz GC056829_ACTCGCTA-CGTCTAAT.R2.fastq.gz	fastq fastq	263635092.0	1046171.0	GSM3730595 r1	0:126 1:126	A:67377756;C:64587136;G:63710559;T:67894292;N:65349	126	126	67377756	64587136	63710559	67894292	65349	SRX5709841	SRS4649012	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.844	0.84157	0.10366	0.10437	0.97656	0.97632	0.50968	0.50944	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	Cancer or Tumor	Cancer or Tumor
51956	51956	SRR8928883	SRX5709840	SRS4649011	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	GC056829 ACTCGCTA CCTAGAGT primary sc	GSM3730594	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 ACTCGCTA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730594	GSM3730594: GC056829 ACTCGCTA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730594	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730594	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_ACTCGCTA-CCTAGAGT.R2.fastq.gz GC056829_ACTCGCTA-CCTAGAGT.R1.fastq.gz	fastq fastq	422834328.0	1677914.0	GSM3730594 r1	0:126 1:126	A:110714199;C:100853575;G:100099181;T:111029373;N:138000	126	126	110714199	100853575	100099181	111029373	138000	SRX5709840	SRS4649011	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.95261	0.95221	0.05884	0.05883	0.97084	0.97104	0.55345	0.55603	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	Cancer or Tumor	Cancer or Tumor
51957	51957	SRR8928882	SRX5709839	SRS4649010	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	GC056829 AAGAGGCA TCGACTAG primary sc	GSM3730593	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 AAGAGGCA TCGACTAG primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730593	GSM3730593: GC056829 AAGAGGCA TCGACTAG primary sc; Danio rerio; RNA Seq	GSM3730593	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730593	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AAGAGGCA-TCGACTAG.R2.fastq.gz GC056829_AAGAGGCA-TCGACTAG.R1.fastq.gz	fastq fastq	197195292.0	782521.0	GSM3730593 r1	0:126 1:126	A:51435119;C:47031488;G:46840206;T:51825650;N:62829	126	126	51435119	47031488	46840206	51825650	62829	SRX5709839	SRS4649010	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.92585	0.92596	0.09446	0.09445	0.92691	0.92685	0.55568	0.55563	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	Cancer or Tumor	Cancer or Tumor
51958	51958	SRR8928881	SRX5709838	SRS4649009	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	GC056829 AAGAGGCA CTCTCTAT primary sc	GSM3730592	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 AAGAGGCA CTCTCTAT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730592	GSM3730592: GC056829 AAGAGGCA CTCTCTAT primary sc; Danio rerio; RNA Seq	GSM3730592	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730592	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AAGAGGCA-CTCTCTAT.R1.fastq.gz GC056829_AAGAGGCA-CTCTCTAT.R2.fastq.gz	fastq fastq	274141224.0	1087862.0	GSM3730592 r1	0:126 1:126	A:69894958;C:67198584;G:66678113;T:70267828;N:101741	126	126	69894958	67198584	66678113	70267828	101741	SRX5709838	SRS4649009	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.89178	0.89179	0.10343	0.10307	0.93022	0.92949	0.56426	0.56865	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	Cancer or Tumor	Cancer or Tumor
51959	51959	SRR8928880	SRX5709837	SRS4649008	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	GC056829 AAGAGGCA CCTAGAGT primary sc	GSM3730591	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 AAGAGGCA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730591	GSM3730591: GC056829 AAGAGGCA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730591	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730591	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AAGAGGCA-CCTAGAGT.R1.fastq.gz GC056829_AAGAGGCA-CCTAGAGT.R2.fastq.gz	fastq fastq	213717924.0	848087.0	GSM3730591 r1	0:126 1:126	A:57133778;C:49850644;G:49020627;T:57640087;N:72788	126	126	57133778	49850644	49020627	57640087	72788	SRX5709837	SRS4649008	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.77974	0.77902	0.12367	0.12391	0.94769	0.94805	0.55807	0.56734	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	Cancer or Tumor	Cancer or Tumor
51960	51960	SRR8928879	SRX5709836	SRS4649007	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	GC056829 AAGAGGCA AAGGAGTA regressed sc	GSM3730590	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GC056829 AAGAGGCA AAGGAGTA regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730590	GSM3730590: GC056829 AAGAGGCA AAGGAGTA regressed sc; Danio rerio; RNA Seq	GSM3730590	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730590	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AAGAGGCA-AAGGAGTA.R1.fastq.gz GC056829_AAGAGGCA-AAGGAGTA.R2.fastq.gz	fastq fastq	196413084.0	779417.0	GSM3730590 r1	0:126 1:126	A:49782320;C:48478812;G:47877291;T:50249615;N:25046	126	126	49782320	48478812	47877291	50249615	25046	SRX5709836	SRS4649007	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.81375	0.81208	0.05174	0.05217	0.97461	0.97433	0.49988	0.49827	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	Cancer or Tumor	Cancer or Tumor
51965	51965	SRR8928874	SRX5709831	SRS4649002	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 CTCTCTAC TCGACTAG regressed psbulk	GSM3730585	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GC056865 CTCTCTAC TCGACTAG regressed 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 regressed triple melanoma	FACS sorting of 5 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730585	GSM3730585: GC056865 CTCTCTAC TCGACTAG regressed psbulk; Danio rerio; RNA Seq	GSM3730585	1	FACS sorting of 5 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730585	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_CTCTCTAC-TCGACTAG.R1.fastq.gz GC056865_CTCTCTAC-TCGACTAG.R2.fastq.gz	fastq fastq	382889304.0	1519402.0	GSM3730585 r1	0:126 1:126	A:100806569;C:89306900;G:88726323;T:104019607;N:29905	126	126	100806569	89306900	88726323	104019607	29905	SRX5709831	SRS4649002	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.75095	0.75214	0.15209	0.15428	0.88434	0.88412	0.54635	0.55778	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	Cancer or Tumor	Cancer or Tumor
51968	51968	SRR8928871	SRX5709828	SRS4648999	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 CGAGGCTG TTCTAGCT primary psbulk	GSM3730582	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056865 CGAGGCTG TTCTAGCT primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730582	GSM3730582: GC056865 CGAGGCTG TTCTAGCT primary psbulk; Danio rerio; RNA Seq	GSM3730582	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730582	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_CGAGGCTG-TTCTAGCT.R1.fastq.gz GC056865_CGAGGCTG-TTCTAGCT.R2.fastq.gz	fastq fastq	356294232.0	1413866.0	GSM3730582 r1	0:126 1:126	A:96219155;C:80375732;G:79844020;T:99829428;N:25897	126	126	96219155	80375732	79844020	99829428	25897	SRX5709828	SRS4648999	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8387	0.83908	0.10871	0.11056	0.91494	0.9152	0.61203	0.61334	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	Cancer or Tumor	Cancer or Tumor
51970	51970	SRR8928869	SRX5709826	SRS4648997	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 ACTGAGCG TTCTAGCT primary psbulk	GSM3730580	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056865 ACTGAGCG TTCTAGCT primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730580	GSM3730580: GC056865 ACTGAGCG TTCTAGCT primary psbulk; Danio rerio; RNA Seq	GSM3730580	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730580	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_ACTGAGCG-TTCTAGCT.R1.fastq.gz GC056865_ACTGAGCG-TTCTAGCT.R2.fastq.gz	fastq fastq	639083592.0	2536046.0	GSM3730580 r1	0:126 1:126	A:175441090;C:142969300;G:142251285;T:178375399;N:46518	126	126	175441090	142969300	142251285	178375399	46518	SRX5709826	SRS4648997	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93288	0.93362	0.05973	0.06032	0.91575	0.91626	0.60299	0.6131	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	Cancer or Tumor	Cancer or Tumor
51972	51972	SRR8928867	SRX5709824	SRS4648995	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	GC056829 TAGGCATG TCGACTAG primary psbulk	GSM3730578	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056829 TAGGCATG TCGACTAG primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730578	GSM3730578: GC056829 TAGGCATG TCGACTAG primary psbulk; Danio rerio; RNA Seq	GSM3730578	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730578	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGGCATG-TCGACTAG.R1.fastq.gz GC056829_TAGGCATG-TCGACTAG.R2.fastq.gz	fastq fastq	134964900.0	535575.0	GSM3730578 r1	0:126 1:126	A:35087288;C:32577677;G:32061705;T:35189618;N:48612	126	126	35087288	32577677	32061705	35189618	48612	SRX5709824	SRS4648995	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.94555	0.94623	0.05263	0.05253	0.79003	0.79064	0.54612	0.54159	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	Cancer or Tumor	Cancer or Tumor
51973	51973	SRR8928866	SRX5709823	SRS4648994	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	GC056829 TAGGCATG CTCTCTAT primary psbulk	GSM3730577	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056829 TAGGCATG CTCTCTAT primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730577	GSM3730577: GC056829 TAGGCATG CTCTCTAT primary psbulk; Danio rerio; RNA Seq	GSM3730577	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730577	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TAGGCATG-CTCTCTAT.R1.fastq.gz GC056829_TAGGCATG-CTCTCTAT.R2.fastq.gz	fastq fastq	160198164.0	635707.0	GSM3730577 r1	0:126 1:126	A:41710067;C:38460475;G:38184788;T:41781543;N:61291	126	126	41710067	38460475	38184788	41781543	61291	SRX5709823	SRS4648994	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.9374	0.93605	0.04665	0.04663	0.81527	0.81586	0.5927	0.58806	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	Cancer or Tumor	Cancer or Tumor
51975	51975	SRR8928864	SRX5709821	SRS4648992	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	GC056829 GGACTCCT TCGACTAG primary psbulk	GSM3730575	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056829 GGACTCCT TCGACTAG primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730575	GSM3730575: GC056829 GGACTCCT TCGACTAG primary psbulk; Danio rerio; RNA Seq	GSM3730575	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730575	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGACTCCT-TCGACTAG.R1.fastq.gz GC056829_GGACTCCT-TCGACTAG.R2.fastq.gz	fastq fastq	42904512.0	170256.0	GSM3730575 r1	0:126 1:126	A:11188431;C:10266151;G:10042286;T:11394194;N:13450	126	126	11188431	10266151	10042286	11394194	13450	SRX5709821	SRS4648992	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.93379	0.93384	0.04834	0.04915	0.79995	0.79977	0.54777	0.53725	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	Cancer or Tumor	Cancer or Tumor
51976	51976	SRR8928863	SRX5709820	SRS4648991	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	GC056829 GGACTCCT CTCTCTAT primary psbulk	GSM3730574	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GC056829 GGACTCCT CTCTCTAT primary 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 primary triple melanoma	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from primary triple melanoma	GSM3730574	GSM3730574: GC056829 GGACTCCT CTCTCTAT primary psbulk; Danio rerio; RNA Seq	GSM3730574	1	FACS sorting of 50 GFP+ living cells from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730574	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_GGACTCCT-CTCTCTAT.R1.fastq.gz GC056829_GGACTCCT-CTCTCTAT.R2.fastq.gz	fastq fastq	80830260.0	320755.0	GSM3730574 r1	0:126 1:126	A:20873744;C:19493970;G:19167382;T:21266422;N:28742	126	126	20873744	19493970	19167382	21266422	28742	SRX5709820	SRS4648991	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.91236	0.91153	0.062	0.0611	0.79821	0.79823	0.56105	0.5664	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	Cancer or Tumor	Cancer or Tumor
51978	51978	SRR8928861	SRX5709818	SRS4648989	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	GC056829 AGGCAGAA CTATTAAG regressed psbulk	GSM3730572	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GC056829 AGGCAGAA CTATTAAG regressed 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 regressed triple melanoma	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730572	GSM3730572: GC056829 AGGCAGAA CTATTAAG regressed psbulk; Danio rerio; RNA Seq	GSM3730572	1	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730572	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_AGGCAGAA-CTATTAAG.R1.fastq.gz GC056829_AGGCAGAA-CTATTAAG.R2.fastq.gz	fastq fastq	62372016.0	247508.0	GSM3730572 r1	0:126 1:126	A:16874800;C:14168305;G:14057126;T:17255676;N:16109	126	126	16874800	14168305	14057126	17255676	16109	SRX5709818	SRS4648989	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.90702	0.90864	0.08229	0.0825	0.8396	0.84007	0.53586	0.5374	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	Cancer or Tumor	Cancer or Tumor
51979	51979	SRR8928857	SRX5709817	SRS4648988	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	Regressed 40	GSM3730571	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 40	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730571	GSM3730571: Regressed 40; Danio rerio; RNA Seq	GSM3730571	1	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT40_S25_L001_R2_001.fastq.gz JT40_S25_L001_R1_001.fastq.gz	fastq fastq	1801141375.0	11944731.0	GSM3730571 r1	0:75.39 1:75.40	A:534184902;C:348794551;G:363388539;T:554447659;N:325724	75	75	534184902	348794551	363388539	554447659	325724	SRX5709817	SRS4648988	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88729	0.88809	0.38897	0.39243	0.94945	0.94929	0.51657	0.52412	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51980	51980	SRR8928858	SRX5709817	SRS4648988	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	Regressed 40	GSM3730571	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 40	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730571	GSM3730571: Regressed 40; Danio rerio; RNA Seq	GSM3730571	1	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT40_S25_L002_R2_001.fastq.gz JT40_S25_L002_R1_001.fastq.gz	fastq fastq	1821054506.0	12075079.0	GSM3730571 r2	0:75.40 1:75.41	A:539114731;C:352662349;G:367769875;T:561213706;N:293845	75	75	539114731	352662349	367769875	561213706	293845	SRX5709817	SRS4648988	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88703	0.88826	0.38981	0.39187	0.94828	0.94961	0.51163	0.52669	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51981	51981	SRR8928859	SRX5709817	SRS4648988	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	Regressed 40	GSM3730571	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 40	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730571	GSM3730571: Regressed 40; Danio rerio; RNA Seq	GSM3730571	1	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT40_S25_L003_R1_001.fastq.gz JT40_S25_L003_R2_001.fastq.gz	fastq fastq	1772127786.0	11751897.0	GSM3730571 r3	0:75.39 1:75.40	A:525172311;C:342822057;G:357172825;T:546677963;N:282630	75	75	525172311	342822057	357172825	546677963	282630	SRX5709817	SRS4648988	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88735	0.88771	0.38787	0.39001	0.94854	0.94957	0.5282	0.52582	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51982	51982	SRR8928860	SRX5709817	SRS4648988	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	Regressed 40	GSM3730571	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 40	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730571	GSM3730571: Regressed 40; Danio rerio; RNA Seq	GSM3730571	1	FACS sorting of 11 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730571	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT40_S25_L004_R2_001.fastq.gz JT40_S25_L004_R1_001.fastq.gz	fastq fastq	1738535209.0	11530020.0	GSM3730571 r4	0:75.39 1:75.40	A:515749195;C:336077168;G:350592062;T:535829458;N:287326	75	75	515749195	336077168	350592062	535829458	287326	SRX5709817	SRS4648988	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.88747	0.88844	0.38864	0.39083	0.94828	0.94897	0.51074	0.51407	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51983	51983	SRR8928853	SRX5709816	SRS4648987	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	Regressed 69	GSM3730570	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 69	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730570	GSM3730570: Regressed 69; Danio rerio; RNA Seq	GSM3730570	1	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730570	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT69_S62_L001_R1_001.fastq.gz JT69_S62_L001_R2_001.fastq.gz	fastq fastq	16334997.0	108934.0	GSM3730570 r1	0:74.96 1:74.99	A:4534140;C:3650881;G:3808762;T:4325331;N:15883	74	74	4534140	3650881	3808762	4325331	15883	SRX5709816	SRS4648987	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.8369	0.83796	0.19619	0.19889	0.89376	0.89443	0.57758	0.59043	73	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51984	51984	SRR8928854	SRX5709816	SRS4648987	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	Regressed 69	GSM3730570	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 69	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730570	GSM3730570: Regressed 69; Danio rerio; RNA Seq	GSM3730570	1	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730570	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT69_S62_L002_R1_001.fastq.gz JT69_S62_L002_R2_001.fastq.gz	fastq fastq	16561704.0	110415.0	GSM3730570 r2	0:74.98 1:75.01	A:4592662;C:3696821;G:3868413;T:4389459;N:14349	74	75	4592662	3696821	3868413	4389459	14349	SRX5709816	SRS4648987	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83698	0.83781	0.19133	0.19527	0.89116	0.89388	0.59259	0.59331	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51985	51985	SRR8928855	SRX5709816	SRS4648987	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	Regressed 69	GSM3730570	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 69	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730570	GSM3730570: Regressed 69; Danio rerio; RNA Seq	GSM3730570	1	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730570	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT69_S62_L003_R1_001.fastq.gz JT69_S62_L003_R2_001.fastq.gz	fastq fastq	15543574.0	103640.0	GSM3730570 r3	0:74.97 1:75.01	A:4321807;C:3467617;G:3629770;T:4110592;N:13788	74	75	4321807	3467617	3629770	4110592	13788	SRX5709816	SRS4648987	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83387	0.83619	0.19157	0.19605	0.89469	0.89749	0.59636	0.59414	75	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51986	51986	SRR8928856	SRX5709816	SRS4648987	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	Regressed 69	GSM3730570	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 69	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730570	GSM3730570: Regressed 69; Danio rerio; RNA Seq	GSM3730570	1	FACS sorting of 10 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730570	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT69_S62_L004_R1_001.fastq.gz JT69_S62_L004_R2_001.fastq.gz	fastq fastq	15235435.0	101657.0	GSM3730570 r4	0:74.92 1:74.95	A:4230280;C:3398938;G:3567492;T:4023835;N:14890	74	74	4230280	3398938	3567492	4023835	14890	SRX5709816	SRS4648987	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.83411	0.83193	0.19469	0.19588	0.89404	0.89574	0.58184	0.59189	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51987	51987	SRR8928849	SRX5709815	SRS4648986	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	Regressed 68	GSM3730569	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 68	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730569	GSM3730569: Regressed 68; Danio rerio; RNA Seq	GSM3730569	1	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730569	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT68_S55_L001_R1_001.fastq.gz JT68_S55_L001_R2_001.fastq.gz	fastq fastq	31456779.0	208912.0	GSM3730569 r1	0:75.28 1:75.30	A:7817535;C:7969610;G:8108415;T:7552871;N:8348	75	75	7817535	7969610	8108415	7552871	8348	SRX5709815	SRS4648986	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.80625	0.79763	0.41833	0.42606	0.82073	0.82775	0.60581	0.59459	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51988	51988	SRR8928850	SRX5709815	SRS4648986	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	Regressed 68	GSM3730569	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 68	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730569	GSM3730569: Regressed 68; Danio rerio; RNA Seq	GSM3730569	1	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730569	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT68_S55_L002_R1_001.fastq.gz JT68_S55_L002_R2_001.fastq.gz	fastq fastq	31694274.0	210438.0	GSM3730569 r2	0:75.30 1:75.31	A:7856831;C:8031333;G:8180981;T:7616805;N:8324	75	75	7856831	8031333	8180981	7616805	8324	SRX5709815	SRS4648986	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.80745	0.79957	0.41843	0.42865	0.81893	0.82542	0.5835	0.59466	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51989	51989	SRR8928851	SRX5709815	SRS4648986	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	Regressed 68	GSM3730569	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 68	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730569	GSM3730569: Regressed 68; Danio rerio; RNA Seq	GSM3730569	1	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730569	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT68_S55_L003_R1_001.fastq.gz JT68_S55_L003_R2_001.fastq.gz	fastq fastq	30938520.0	205425.0	GSM3730569 r3	0:75.29 1:75.31	A:7620278;C:7891593;G:8029435;T:7390003;N:7211	75	75	7620278	7891593	8029435	7390003	7211	SRX5709815	SRS4648986	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.80463	0.79818	0.42484	0.4343	0.82156	0.82718	0.57393	0.57341	75	75	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51990	51990	SRR8928852	SRX5709815	SRS4648986	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	Regressed 68	GSM3730569	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	Regressed 68	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 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 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 regressed triple melanoma	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cells from regressed triple melanoma	GSM3730569	GSM3730569: Regressed 68; Danio rerio; RNA Seq	GSM3730569	1	FACS sorting of 50 GFP+ living cells from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730569	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP193005	JT68_S55_L004_R1_001.fastq.gz JT68_S55_L004_R2_001.fastq.gz	fastq fastq	30487999.0	202504.0	GSM3730569 r4	0:75.27 1:75.29	A:7508986;C:7770782;G:7923727;T:7275703;N:8801	75	75	7508986	7770782	7923727	7275703	8801	SRX5709815	SRS4648986	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.80737	0.79782	0.42869	0.43773	0.82193	0.82824	0.59611	0.59614	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	poly_a	nextera	sc	single_cell_plate	smartseq	United Kingdom	2019-04-18	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor
51991	51991	SRR8928965	SRX5709814	SRS4648985	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 GGACTCCT TTCTAGCT regressed sc	GSM3730676	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056865 GGACTCCT TTCTAGCT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730676	GSM3730676: GC056865 GGACTCCT TTCTAGCT regressed sc; Danio rerio; RNA Seq	GSM3730676	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730676	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_GGACTCCT-TTCTAGCT.R1.fastq.gz GC056865_GGACTCCT-TTCTAGCT.R2.fastq.gz	fastq fastq	304115868.0	1206809.0	GSM3730676 r1	0:126 1:126	A:77026620;C:73994312;G:73881191;T:79192301;N:21444	126	126	77026620	73994312	73881191	79192301	21444	SRX5709814	SRS4648985	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.57661	0.58153	0.16024	0.16302	0.97049	0.97005	0.55827	0.56035	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	Cancer or Tumor	Cancer or Tumor
51992	51992	SRR8928964	SRX5709813	SRS4648983	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 GCTCATGA TCGACTAG regressed sc	GSM3730675	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056865 GCTCATGA TCGACTAG regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730675	GSM3730675: GC056865 GCTCATGA TCGACTAG regressed sc; Danio rerio; RNA Seq	GSM3730675	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730675	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_GCTCATGA-TCGACTAG.R1.fastq.gz GC056865_GCTCATGA-TCGACTAG.R2.fastq.gz	fastq fastq	246895236.0	979743.0	GSM3730675 r1	0:126 1:126	A:62118946;C:60589480;G:60472618;T:63697273;N:16919	126	126	62118946	60589480	60472618	63697273	16919	SRX5709813	SRS4648983	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.5842	0.58687	0.09548	0.09709	0.97033	0.96984	0.51559	0.52225	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	Cancer or Tumor	Cancer or Tumor
51993	51993	SRR8928963	SRX5709812	SRS4648984	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 ACTCGCTA TTCTAGCT regressed sc	GSM3730674	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056865 ACTCGCTA TTCTAGCT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730674	GSM3730674: GC056865 ACTCGCTA TTCTAGCT regressed sc; Danio rerio; RNA Seq	GSM3730674	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730674	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056865_ACTCGCTA-TTCTAGCT.R1.fastq.gz GC056865_ACTCGCTA-TTCTAGCT.R2.fastq.gz	fastq fastq	633450888.0	2513694.0	GSM3730674 r1	0:126 1:126	A:172169697;C:142735591;G:142048024;T:176451150;N:46426	126	126	172169697	142735591	142048024	176451150	46426	SRX5709812	SRS4648984	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.90617	0.90539	0.1074	0.10879	0.85169	0.85208	0.57984	0.58374	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	Cancer or Tumor	Cancer or Tumor
51994	51994	SRR8928962	SRX5709811	SRS4648982	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	GC056829 TGCAGCTA CGTCTAAT regressed sc	GSM3730673	source name:mitfa:GFP cells from regressed triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GC056829 TGCAGCTA CGTCTAAT regressed sc	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 regressed triple melanoma	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from regressed triple melanoma	GSM3730673	GSM3730673: GC056829 TGCAGCTA CGTCTAAT regressed sc; Danio rerio; RNA Seq	GSM3730673	1	FACS sorting of a single GFP+ living cell from regression site SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730673	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TGCAGCTA-CGTCTAAT.R1.fastq.gz GC056829_TGCAGCTA-CGTCTAAT.R2.fastq.gz	fastq fastq	211512672.0	839336.0	GSM3730673 r1	0:126 1:126	A:53472717;C:52123498;G:51726414;T:54135570;N:54473	126	126	53472717	52123498	51726414	54135570	54473	SRX5709811	SRS4648982	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.84239	0.84133	0.07568	0.07604	0.97512	0.97504	0.47563	0.46606	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	Cancer or Tumor	Cancer or Tumor
51995	51995	SRR8928961	SRX5709810	SRS4648981	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	GC056829 TGCAGCTA CCTAGAGT primary sc	GSM3730672	source name:mitfa:GFP cells from primary triple melanoma\|genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GC056829 TGCAGCTA CCTAGAGT primary sc	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 primary triple melanoma	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	genotype:mitfa:BRAFV600E;mitfavc7;p53M214K\|tissue:GFP+ cell from primary triple melanoma	GSM3730672	GSM3730672: GC056829 TGCAGCTA CCTAGAGT primary sc; Danio rerio; RNA Seq	GSM3730672	1	FACS sorting of a single GFP+ living cell from primary tumour SMARTseq2 Picelli et al 2014 polyA selection cDNA TruSeq or Nextera XT RNA Seq Paired end reads	GEO Accession:GSM3730672	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP193005	GC056829_TGCAGCTA-CCTAGAGT.R1.fastq.gz GC056829_TGCAGCTA-CCTAGAGT.R2.fastq.gz	fastq fastq	380884644.0	1511447.0	GSM3730672 r1	0:126 1:126	A:100150445;C:90424699;G:89533745;T:100642128;N:133627	126	126	100150445	90424699	89533745	100642128	133627	SRX5709810	SRS4648981	SRA876955	GEO	Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC	2	0.9399	0.93887	0.07352	0.07407	0.96301	0.96321	0.53648	0.52077	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	Cancer or Tumor	Cancer or Tumor

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;