metadata: run_metadata: 49 rows where devstage_curation_coarse = "Adult" and tissue_curation

49 rows where devstage_curation_coarse = "Adult" 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.attributes	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
41084	41084	SRR3666784	SRX1845189	SRS1504028	SRP076552	PRJNA325656	Differential gene expression of zebrafish melanocytes and melanomas [RNA seq]	GSE83343	Transcriptome Analysis	We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types	parent bioproject:PRJNA325808	pubmed:29202482	ZF melanoma rep4	GSM2199909	tissue:melanoma\|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4\|age:adult\|cell type:melanoma	ZF melanoma rep4	Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples	melanoma		RNA was harvested from cells using Trizol reagent. Illumina TruSeq	Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS	strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4\|age:adult\|cell type:melanoma	GSM2199909	GSM2199909: ZF melanoma rep4; Danio rerio; RNA Seq	GSM2199909		1	RNA was harvested from cells using Trizol reagent. Illumina TruSeq	GEO Accession:GSM2199909	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP076552		Melanoma_4_R1.fastq.gz Melanoma_4_R2.fastq.gz	fastq fastq	5824407060.0	57102030.0	GSM2199909 r1	0:51 1:51	A:1623471404;C:1272539670;G:1281078941;T:1643101126;N:4215919	51	51	1623471404	1272539670	1281078941	1643101126	4215919	SRX1845189	SRS1504028	SRA433946	GEO	PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts	2	0.9269	0.87875	0.16101	0.15437	0.75601	0.76479	0.52959	0.49449	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41085	41085	SRR3666783	SRX1845188	SRS1504029	SRP076552	PRJNA325656	Differential gene expression of zebrafish melanocytes and melanomas [RNA seq]	GSE83343	Transcriptome Analysis	We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types	parent bioproject:PRJNA325808	pubmed:29202482	ZF melanoma rep3	GSM2199908	tissue:melanoma\|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4\|age:adult\|cell type:melanoma	ZF melanoma rep3	Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples	melanoma		RNA was harvested from cells using Trizol reagent. Illumina TruSeq	Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS	strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4\|age:adult\|cell type:melanoma	GSM2199908	GSM2199908: ZF melanoma rep3; Danio rerio; RNA Seq	GSM2199908		1	RNA was harvested from cells using Trizol reagent. Illumina TruSeq	GEO Accession:GSM2199908	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP076552		Melanoma_3_R1.fastq.gz Melanoma_3_R2.fastq.gz	fastq fastq	6025625112.0	59074756.0	GSM2199908 r1	0:51 1:51	A:1664666728;C:1334918212;G:1342599896;T:1679035262;N:4405014	51	51	1664666728	1334918212	1342599896	1679035262	4405014	SRX1845188	SRS1504029	SRA433946	GEO	PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts	2	0.93254	0.8901	0.13621	0.13127	0.75858	0.76562	0.52486	0.51808	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41086	41086	SRR3666782	SRX1845187	SRS1504027	SRP076552	PRJNA325656	Differential gene expression of zebrafish melanocytes and melanomas [RNA seq]	GSE83343	Transcriptome Analysis	We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types	parent bioproject:PRJNA325808	pubmed:29202482	ZF melanoma rep2	GSM2199907	tissue:melanoma\|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4\|age:adult\|cell type:melanoma	ZF melanoma rep2	Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples	melanoma		RNA was harvested from cells using Trizol reagent. Illumina TruSeq	Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS	strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4\|age:adult\|cell type:melanoma	GSM2199907	GSM2199907: ZF melanoma rep2; Danio rerio; RNA Seq	GSM2199907		1	RNA was harvested from cells using Trizol reagent. Illumina TruSeq	GEO Accession:GSM2199907	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP076552		Melanoma_2_R1.fastq.gz Melanoma_2_R2.fastq.gz	fastq fastq	5820855420.0	57067210.0	GSM2199907 r1	0:51 1:51	A:1608054488;C:1286088047;G:1295801092;T:1626675668;N:4236125	51	51	1608054488	1286088047	1295801092	1626675668	4236125	SRX1845187	SRS1504027	SRA433946	GEO	PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts	2	0.9408	0.88645	0.14414	0.13333	0.76441	0.77291	0.53482	0.53362	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41087	41087	SRR3666780	SRX1845186	SRS1504026	SRP076552	PRJNA325656	Differential gene expression of zebrafish melanocytes and melanomas [RNA seq]	GSE83343	Transcriptome Analysis	We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas. Overall design: Examination of gene expression in two different cell types	parent bioproject:PRJNA325808	pubmed:29202482	ZF melanoma rep1	GSM2199906	tissue:melanoma\|strain:Tgmitfa:BRAFV600E; p53zdf1; Tgmitfa:EGFP; albb4\|age:adult\|cell type:melanoma	ZF melanoma rep1	Star v2.3 was used to align the reads htseq count was used to count mappped reads DESeq2 was used to perform differential gene expression analysis Genome build: Zebrafish Zv9 Supplementary files format and content: tab delimited txt file includes FPKM values for all samples	melanoma		RNA was harvested from cells using Trizol reagent. Illumina TruSeq	Unpigmented EGFP positive melanocytes and melanoma cells were isolated by FACS	strain:Tgmitfa:BRAFV600E;p53zdf1;Tgmitfa:EGFP;albb4\|age:adult\|cell type:melanoma	GSM2199906	GSM2199906: ZF melanoma rep1; Danio rerio; RNA Seq	GSM2199906		1	RNA was harvested from cells using Trizol reagent. Illumina TruSeq	GEO Accession:GSM2199906	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP076552		Melanoma_1_R1.fastq.gz Melanoma_1_R2.fastq.gz	fastq fastq	6005883522.0	58881211.0	GSM2199906 r1	0:51 1:51	A:1674714880;C:1311907155;G:1323946262;T:1691018505;N:4296720	51	51	1674714880	1311907155	1323946262	1691018505	4296720	SRX1845186	SRS1504026	SRA433946	GEO	PMM Bioinformatics Core, Program in Molecular Medicine, University of Massachusetts	2	0.9244	0.87204	0.16657	0.15895	0.74921	0.75688	0.52057	0.51652	51	51	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	United States	2016-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41616	41616	SRR5099113	SRX2415891	SRS1853479	SRP094947	PRJNA357051	Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods	GSE92260	Transcriptome Analysis	we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes rb1 induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB like PNETs Overall design: QuantSeq three prime mRNA sequencing with whole brain tissue wild type WT zebrafish and tumors induced by rb1 TALENs injected zebrafish at xxx mpf		pubmed:28903419	FFPE 2	GSM2424730	source name:tumor 2 induced by rb1 TALENs\|strain:p53M214K\|tissue:tumor tissues 2 induced by rb1 TALENs\|developmental stage:5 mpf	FFPE 2	Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequenceusing fastx trimmer then mapped to danRer10 whole genome using Bowtie2 Read count extraction and nomalization were performed using edgeR. Genome build: danRer10 Supplementary files format and content: FFPE 1.txt and FFPE 2.txt report quantile normalized abundance measurements. Supplementary files format and content: WT.txt report quantile normalized abundance measurements. Column WT1 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 1. Column WT2 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 2.	tumor 2 induced by rb1 TALENs		RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.		strain:p53M214K\|tissue:tumor tissues 2 induced by rb1 TALENs\|developmental stage:5 mpf	GSM2424730	GSM2424730: FFPE 2; Danio rerio; RNA Seq	GSM2424730		1	RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.	GEO Accession:GSM2424730	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP094947		FFPE-2_fastq.gz	fastq	900420050.0	8915050.0	GSM2424730 r1	0:101	A:404381931;C:201118712;G:149335807;T:145550067;N:33533	101		404381931	201118712	149335807	145550067	33533	SRX2415891	SRS1853479	SRA502460	GEO	Research Institute, National Cancer Center	1	0.03639		0.02825		0.9978		0.55688		101		B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Unknown	2016-12-12	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41617	41617	SRR5099112	SRX2415890	SRS1853478	SRP094947	PRJNA357051	Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods	GSE92260	Transcriptome Analysis	we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes rb1 induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB like PNETs Overall design: QuantSeq three prime mRNA sequencing with whole brain tissue wild type WT zebrafish and tumors induced by rb1 TALENs injected zebrafish at xxx mpf		pubmed:28903419	FFPE 1	GSM2424729	source name:tumor 1 induced by rb1 TALENs\|strain:p53M214K\|tissue:tumor tissues 1 induced by rb1 TALENs\|developmental stage:5 mpf	FFPE 1	Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequenceusing fastx trimmer then mapped to danRer10 whole genome using Bowtie2 Read count extraction and nomalization were performed using edgeR. Genome build: danRer10 Supplementary files format and content: FFPE 1.txt and FFPE 2.txt report quantile normalized abundance measurements. Supplementary files format and content: WT.txt report quantile normalized abundance measurements. Column WT1 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 1. Column WT2 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 2.	tumor 1 induced by rb1 TALENs		RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.		strain:p53M214K\|tissue:tumor tissues 1 induced by rb1 TALENs\|developmental stage:5 mpf	GSM2424729	GSM2424729: FFPE 1; Danio rerio; RNA Seq	GSM2424729		1	RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols.	GEO Accession:GSM2424729	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP094947		FFPE-1_fastq.gz	fastq	985654556.0	9758956.0	GSM2424729 r1	0:101	A:642158389;C:109642019;G:103170689;T:130633868;N:49591	101		642158389	109642019	103170689	130633868	49591	SRX2415890	SRS1853478	SRA502460	GEO	Research Institute, National Cancer Center	1	0.71847		0.59813		0.9376		0.57167		101		B		usable mapping rate	illumina	nextseq	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown	Unknown	2016-12-12	Adult	Adult	Cancer or Tumor	Cancer or Tumor
41811	41811	SRR5196075	SRX2511746	SRS1935439	SRP097636	PRJNA362941	Transcriptomic analyses of Kras induced zebrafish liver cancer	GSE93965	Transcriptome Analysis	The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.		pubmed:31827597	CarcinomaM	GSM2465779	source name:Hepatocellular carcinoma of transgenic fishes post mifeprist1 withdrawal\|tissue:Hepatocellular carcinoma\|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line	CarcinomaM	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample	Hepatocellular carcinoma of transgenic fishes post mifepristone withdrawal	One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.	mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample		tissue:Hepatocellular carcinoma\|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line	GSM2465779	GSM2465779: CarcinomaM; Danio rerio; RNA Seq	GSM2465779		1	mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample	GEO Accession:GSM2465779	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP097636		solid_SAGE_6T2_F3.csfasta.gz solid_SAGE_6T2_F3_QV.qual.gz	SOLiD_native SOLiD_native	818910190.0	23397434.0	GSM2465779 r1	0:35	0:347259734;1:164743259;2:162029194;3:130508344;.:14369659	35							SRX2511746	SRS1935439	SRA530985	GEO	The Biomedical Center	1	0.03756		0.00615		0.99928		0.91338		35		B		usable mapping rate	legacy	early	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2017-01-23	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
41812	41812	SRR5196074	SRX2511745	SRS1935438	SRP097636	PRJNA362941	Transcriptomic analyses of Kras induced zebrafish liver cancer	GSE93965	Transcriptome Analysis	The krasV12 induced tumor progression was conducted on 100 transgenic fishes maintained in water containing 2µM mifepristone. Gross morphological and histological analyses were weekly performed on 15 randomly selected fishes to monitor tumor development. These analyses showed robust development of hepatocellular adenoma within 4 weeks of induction. Observation of tumor development and staging of tumorigenesis was conducted as described. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water. Histological examination revealed tumor shrinkage showing extensive scarring at the peripheral and focal tumor regions. Notably complete tumor regression with scarred fibrosis of the former tumor tissue was observed post 4 weeks of mifepristone withdrawal. Overall design: Liver tumors from mifipristone induced transgenic fishes with hepatocellular adenoma and carcinoma livers of transgenic fishes post mifepristone withdrawal and normal livers from non induced and induced transgenic fishes were pooled separately and collected for RNA isolation and sequencing.		pubmed:31827597	Carcinoma	GSM2465778	source name:Hepatocellular carcinoma of transgenic fishes\|tissue:Hepatocellular carcinoma\|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line	Carcinoma	The SOLiD generated RNA Seq reads was in 27 bp length and an initial filtering process was taken to remove any non desirable contamination sequences. The reads were mapped to the zebrafish NCBI RefSeq Reference Sequence mRNA database with a criterion of maximum 2 nucleotide mismatches. The expression levels of mapped transcripts were normalized into transcript per whole amount of mapped transcript. Genome build: danRer7 Supplementary files format and content: tab delimited text files include TPM values for each Sample	Hepatocellular carcinoma of transgenic fishes	One mpf transgenic fish was treated at 2uM mifepriston to induce liver tumorigenesis. For tumor regression the group of 15 fishes with HCC was transferred to mifepristone free water.	mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample		tissue:Hepatocellular carcinoma\|genotype:Tgfabp10:LexPR LexA:EGFP; cryB:mCherry NLS Cre; fabp10:loxP mCherry loxP EGFP krasV12 line	GSM2465778	GSM2465778: Carcinoma; Danio rerio; RNA Seq	GSM2465778		1	mRNA was purified using Dynabeads OligodT EcoP Invitrogen Resultant cDNA was digested by NlaIII and EcoP15I to result in a 27 nucleotides cDNA tag between the two sequencing adapters. 3′ RNA SAGE serial analysis of gene expression sequencing was performed on ABI SOLiD platform by Mission Biotech Taiwan according to manufacturer’s protocol and 10–23 million reads were generated from each sample	GEO Accession:GSM2465778	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ABI_SOLID	AB SOLiD System 3.0	SRP097636		solid_SAGE_6T1_F3.csfasta.gz solid_SAGE_6T1_F3_QV.qual.gz	SOLiD_native SOLiD_native	761241005.0	21749743.0	GSM2465778 r1	0:35	0:306840116;1:164725874;2:160786359;3:126370697;.:2517959	35							SRX2511745	SRS1935438	SRA530985	GEO	The Biomedical Center	1	0.0543		0.00668		0.9988		0.95092		35		B		usable mapping rate	legacy	early	unknown	poly_a	unknown	bulk	unknown	unknown	Unknown	2017-01-23	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
61554	61554	SRR14804251	SRX11137027	SRS9200152	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Nuc seq	GSM5380072	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single nucleus suspension	Nuc seq	Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes.	Zebrafish melanomas BRAF V600E		Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.		sample type:Single nucleus suspension	GSM5380072	GSM5380072: Nuc seq; Danio rerio; RNA Seq	GSM5380072		1	Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.	GEO Accession:GSM5380072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287858		2498_Zebrafish_IGO_11175_B_17_S16_L001_R1_001.fastq-001.gz 2498_Zebrafish_IGO_11175_B_17_S16_L001_R2_001.fastq-003.gz	fastq fastq	16881438541.0	139516021.0	GSM5380072 r1	0:29 1:92	A:4751346944;C:3672149977;G:3866179079;T:4591370192;N:392349	29	92	4751346944	3672149977	3866179079	4591370192	392349	SRX11137027	SRS9200152	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.0064	0.82934	0.00273	0.1289	0.99462	0.75615	0.43651	0.54303	29	92	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61555	61555	SRR14804252	SRX11137027	SRS9200152	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Nuc seq	GSM5380072	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single nucleus suspension	Nuc seq	Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes.	Zebrafish melanomas BRAF V600E		Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.		sample type:Single nucleus suspension	GSM5380072	GSM5380072: Nuc seq; Danio rerio; RNA Seq	GSM5380072		1	Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.	GEO Accession:GSM5380072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287858		2498_Zebrafish_IGO_11175_B_17_S16_L002_R1_001.fastq-002.gz 2498_Zebrafish_IGO_11175_B_17_S16_L002_R2_001.fastq-004.gz	fastq fastq	16950408541.0	140086021.0	GSM5380072 r2	0:29 1:92	A:4767053400;C:3688816562;G:3885746735;T:4608355293;N:436551	29	92	4767053400	3688816562	3885746735	4608355293	436551	SRX11137027	SRS9200152	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00657	0.8291	0.00269	0.12832	0.9946	0.75657	0.45883	0.54175	29	92	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61556	61556	SRR14804253	SRX11137027	SRS9200152	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Nuc seq	GSM5380072	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single nucleus suspension	Nuc seq	Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes.	Zebrafish melanomas BRAF V600E		Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.		sample type:Single nucleus suspension	GSM5380072	GSM5380072: Nuc seq; Danio rerio; RNA Seq	GSM5380072		1	Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.	GEO Accession:GSM5380072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287858		2498_Zebrafish_HTO_IGO_11175_B_18_S18_L001_R1_001.fastq.gz 2498_Zebrafish_HTO_IGO_11175_B_18_S18_L001_R2_001.fastq-004.gz	fastq fastq	6220719747.0	51410907.0	GSM5380072 r3	0:29 1:92	A:3158621534;C:796885709;G:1264774949;T:1000285734;N:151821	29	92	3158621534	796885709	1264774949	1000285734	151821	SRX11137027	SRS9200152	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00012	0.14112	9e-05	0.135	0.99993	0.99953	0.33333	0.55555	29	92	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61557	61557	SRR14804254	SRX11137027	SRS9200152	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Nuc seq	GSM5380072	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single nucleus suspension	Nuc seq	Illumina RTA v2 software was used for basecalling and quality determination. The 10x Genomics three prime v3 raw FASTQ data was processed using 10X Genomics proprietary CellRanger v5.0.1 pipeline. Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics three prime GEX v3 data: output of CellRanger pipeline including gene expression matrix features and barcodes.	Zebrafish melanomas BRAF V600E		Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3’ Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer’s instructions.		sample type:Single nucleus suspension	GSM5380072	GSM5380072: Nuc seq; Danio rerio; RNA Seq	GSM5380072		1	Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. The tissue was then ground in a Dounce homogenizer on ice in Nuclei EZ Prep Lysis Buffer Sigma Aldrich #NUC101. The nuclear suspension was then spun down at 4°C 500g 5 min. post resuspending the pellet in 1 mL wash buffer 250 mM sucrose 50 mM citric acid 1% BSA 20 mM DTT 0.2U/µL RNAse inhibitor the sample was again spun at 4°C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4°C to isolate individual nuclei using a BD FACSAria III cell sorter BD Biosciences. Approximately equal numbers of GFP+ tumor and GFP microenvironment nuclei were collected. Equal numbers of sorted GFP+ tumor and GFP microenvironment nuclei were centrifuged at 600g for 5 minutes at 4°C. Droplet based snRNA seq was performed using the Chromium Single Cell three prime Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell three prime Chip G 10X Genomics. Approximately 12 000 nuclei were encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.	GEO Accession:GSM5380072	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP287858		2498_Zebrafish_HTO_IGO_11175_B_18_S18_L002_R1_001.fastq.gz 2498_Zebrafish_HTO_IGO_11175_B_18_S18_L002_R2_001.fastq-003.gz	fastq fastq	6140782307.0	50750267.0	GSM5380072 r4	0:29 1:92	A:3118957514;C:786290907;G:1248322710;T:987056069;N:155107	29	92	3118957514	786290907	1248322710	987056069	155107	SRX11137027	SRS9200152	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00011	0.13904	9e-05	0.13261	0.99995	0.99959	1.0	0.42857	29	92	T	B	sc-like readlen	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-06-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61558	61558	SRR12851622	SRX9318589	SRS7543399	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	SingleCell F	GSM4838135	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single cell suspension	SingleCell F	Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes.	Zebrafish melanomas BRAF V600E		For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…		sample type:Single cell suspension	GSM4838135	GSM4838135: SingleCell F; Danio rerio; RNA Seq	GSM4838135		1	For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m…	GEO Accession:GSM4838135	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP287858		10X_SingleCell_Sample_F_S1_L000_R1_001.fastq.gz 10X_SingleCell_Sample_F_S1_L000_R2_001.fastq.gz	fastq fastq	44547263840.0	278420399.0	GSM4838135 r1	0:28 1:132	A:12810925700;C:9421837786;G:9930050611;T:12378989254;N:5460489	28	132	12810925700	9421837786	9930050611	12378989254	5460489	SRX9318589	SRS7543399	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00339	0.91854	0.00135	0.1624	0.99494	0.79744	0.35078	0.56648	28	132	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-10-20	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61559	61559	SRR12851621	SRX9318588	SRS7543398	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	SingleCell E	GSM4838134	tissue:Zebrafish melanomas BRAF V600E\|sample type:Single cell suspension	SingleCell E	Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes.	Zebrafish melanomas BRAF V600E		For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…		sample type:Single cell suspension	GSM4838134	GSM4838134: SingleCell E; Danio rerio; RNA Seq	GSM4838134		1	For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m…	GEO Accession:GSM4838134	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP287858		10X_SingleCell_Sample_E_S1_L000_R1_001.fastq.gz 10X_SingleCell_Sample_E_S1_L000_R2_001.fastq.gz	fastq fastq	44430354080.0	277689713.0	GSM4838134 r1	0:28 1:132	A:12355044923;C:9923404810;G:10323616312;T:11822807950;N:5480085	28	132	12355044923	9923404810	10323616312	11822807950	5480085	SRX9318588	SRS7543398	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00204	0.9315	0.00092	0.09404	0.9964	0.83027	0.40865	0.54937	28	132	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-10-20	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61560	61560	SRR12851620	SRX9318587	SRS7543397	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Visium C	GSM4838133	tissue:Zebrafish melanomas BRAF V600E\|sample type:Tissue cryosections	Visium C	Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment.	Zebrafish melanomas BRAF V600E		For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…		sample type:Tissue cryosections	GSM4838133	GSM4838133: Visium C; Danio rerio; RNA Seq	GSM4838133		1	For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m…	GEO Accession:GSM4838133	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP287858		Visium_Sample_C_S3_L000_R1_001.fastq.gz Visium_Sample_C_S3_L000_R2_001.fastq.gz	fastq fastq	13306156376.0	89906462.0	GSM4838133 r1	0:28 1:120	A:4587866955;C:2519579655;G:2801896206;T:3387510435;N:9303125	28	120	4587866955	2519579655	2801896206	3387510435	9303125	SRX9318587	SRS7543397	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.0035	0.64737	0.00263	0.05262	0.99734	0.91959	0.55029	0.53722	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-10-20	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61561	61561	SRR12851619	SRX9318586	SRS7543396	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Visium B	GSM4838132	tissue:Zebrafish melanomas BRAF V600E\|sample type:Tissue cryosections	Visium B	Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment.	Zebrafish melanomas BRAF V600E		For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…		sample type:Tissue cryosections	GSM4838132	GSM4838132: Visium B; Danio rerio; RNA Seq	GSM4838132		1	For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m…	GEO Accession:GSM4838132	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP287858		Visium_Sample_B_S2_L000_R2_001.fastq.gz Visium_Sample_B_S2_L000_R1_001.fastq.gz	fastq fastq	9316849676.0	62951687.0	GSM4838132 r1	0:28 1:120	A:2870712770;C:1917570201;G:2077620827;T:2444412876;N:6533002	28	120	2870712770	1917570201	2077620827	2444412876	6533002	SRX9318586	SRS7543396	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00194	0.80482	0.00091	0.06131	0.99711	0.90325	0.5736	0.52314	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-10-20	Adult	Adult	Cancer or Tumor	Cancer or Tumor
61562	61562	SRR12851618	SRX9318585	SRS7543395	SRP287858	PRJNA670235	Spatially resolved transcriptomics reveals the architecture of the tumor microenvironment interface	GSE159709	Transcriptome Analysis	Cancer cells interact with a wide variety of other cell types but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single cell RNA seq scRNA seq has helped define these TME cell types it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here we integrate spatial transcriptomics with scRNA seq to define the architecture and nature of nascent tumor and surrounding microenvironment cells as they come into contact through the process of invasion. Using a well defined transgenic zebrafish model of BRAFV600E driven melanoma we identify a transcriptionally unique “interface” cluster localized at the boundary between tumor cells and surrounding tissues. Using an unbiased data driven approach we identify spatially patterned gene modules specific to the interface and show that the interface is a distinct transcriptional entity that histologically resembles the microenvironment but transcriptionally resembles the tumor. By complementing ST with scRNA seq we demonstrate that the interface is composed of specialized tumor and microenvironment cells. Both cell types in the interface upregulate a common set of cilia genes and we find enrichment of cilia proteins only where the tumor meets the TME. Cilia gene expression is regulated by ETS family transcription factors which normally act to suppress their expression outside of this region. This unique ETS driven interface transcriptional state is conserved across ten different human patient samples suggesting this is a conserved feature of human melanoma. Taken together our results demonstrate the power of spatial and single cell transcriptomics techniques in uncovering novel biological mechanisms that drive tumor invasion into new tissues. Overall design: Spatial transcriptomics Visium platform of zebrafish bearing BRAF V600E driven melanomas. Single cell RNA seq 10X Genomics v3 of two such zebrafish. Single nucleus RNA seq 10X Genomics v3 of three suc…		pubmed:34725363	Visium A	GSM4838131	tissue:Zebrafish melanomas BRAF V600E\|sample type:Tissue cryosections	Visium A	Illumina RTA v2 software was used for basecalling and quality determination. The Visium raw FASTQ data was processed using 10X Genomics proprietary SpaceRanger v1.0.0 pipeline. The single cell RNA seq raw FASTQ data was processed using the 10X Genomics proprietary CellRanger v3.1.0 pipeline Genome build: GRCz10.88 Supplementary files format and content: For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline including gene expression and spatial contents. For 10x Genomics single cell RNA Seq: output of CellRanger pipeline including gene expression features and barcodes. Supplementary files format and content: * image.tif: Tissue section used for Spatial Transcriptomics experiment.	Zebrafish melanomas BRAF V600E		For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3’ GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and mounted in…		sample type:Tissue cryosections	GSM4838131	GSM4838131: Visium A; Danio rerio; RNA Seq	GSM4838131		1	For spatial transcriptomics using the Visium platform from 10X genomics: Adult tumor bearing fish were euthanized on ice and washed in 1X PBS. post dissection of the head and tail the remaining tissue was equilibrated in cold OCT for 2 minutes before transfer to a tissue mold filled with fresh OCT for snap freezing in liquid nitrogen chilled isopentane. Tissue blocks were stored at 80°C. For cryosectioning both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16°C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 µm and immediately placed on the ST slide Visium Spatial Gene Expression Slides 10X Genomics. ST slides containing sections were stored at 80°C for a maximum of one week before use. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Adult tumor bearing fish were dissected to obtain only the tumor and surrounding tissues i.e head and tail were removed. Tissue was minced with a fresh scalpel and incubated in 0.16 mg/mL liberase Sigma Aldrich #5401020001 in 0.9X PBS for 15 minutes at RT. Tissue was then further dissociated by repeated pipetting with a wide bore P1000 followed by incubation for an additional 15 minutes at RT. post adding 500 uL FBS to stop the dissociation reaction samples were filtered through a 70 µm filter and centrifuged at 500g for 5 minutes at RT. The resulting pellet was resuspended in DMEM supplemented with 2% FBS and cells were sorted at room temperature to remove debris and doublets using a BD FACSAria III cell sorter BD Biosciences. Equal numbers of GFP+ tumor and GFP macroenvironment cells were collected. For spatial transcriptomics using the Visium platform from 10X genomics: Samples were processed according to the Visium Spatial Gene Expression User Guide 10X Genomics and all reagents were from the Visium Spatial Gene Expression Kit 10X Genomics. Briefly sections were fixed in chilled methanol for 30 min at 20°C stained with hematoxylin and eosin and m…	GEO Accession:GSM4838131	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP287858		Visium_Sample_A_S1_L001_R1_001.fastq.gz Visium_Sample_A_S1_L001_R2_001.fastq.gz	fastq fastq	8186801004.0	55316223.0	GSM4838131 r1	0:28 1:120	A:3045741900;C:1541903021;G:1757255221;T:1836190790;N:5710072	28	120	3045741900	1541903021	1757255221	1836190790	5710072	SRX9318585	SRS7543395	SRA1145723	GEO	Memorial Sloan Kettering Cancer Center	2	0.00549	0.65605	0.00319	0.10569	0.99734	0.93545	0.52914	0.56848	28	120	T	B	sc-like readlen	illumina	nextseq	unknown	random_priming	unknown	sc	single_cell_droplet	10x	United States	2020-10-20	Adult	Adult	Cancer or Tumor	Cancer or Tumor
65013	65013	SRR14902693	SRX11217415	SRS9271514	SRP325444	PRJNA741108	Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq]	GSE178801	Transcriptome Analysis	With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.	parent bioproject:PRJNA741103	pubmed:34791221	MA3C RNAseq	GSM5397960	source name:Sorted melanoma tumor\|genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma	MA3C RNAseq	Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as	Sorted melanoma tumor		FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit		genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma\|run #:1	GSM5397960	GSM5397960: MA3C RNAseq; Danio rerio; RNA Seq	GSM5397960		1	FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit	GEO Accession:GSM5397960	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP325444		MA3C.fq.gz	fastq	1678480250.0	33569605.0	GSM5397960 r1	0:50 1:0	A:463941895;C:370163467;G:364477555;T:478705617;N:1191716	50	0	463941895	370163467	364477555	478705617	1191716	SRX11217415	SRS9271514	SRA1250059	GEO	Kaufman, Oncology, Washington University in St. Louis	1	0.90303		0.16625		0.74696		0.55133		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2021-06-24	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
65014	65014	SRR14902692	SRX11217414	SRS9271513	SRP325444	PRJNA741108	Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq]	GSE178801	Transcriptome Analysis	With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.	parent bioproject:PRJNA741103	pubmed:34791221	MA3B RNAseq	GSM5397959	source name:Sorted melanoma tumor\|genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma	MA3B RNAseq	Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as	Sorted melanoma tumor		FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit		genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma\|run #:1	GSM5397959	GSM5397959: MA3B RNAseq; Danio rerio; RNA Seq	GSM5397959		1	FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit	GEO Accession:GSM5397959	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP325444		MA3B.fq.gz	fastq	1437189100.0	28743782.0	GSM5397959 r1	0:50 1:0	A:398259972;C:317724608;G:311519412;T:408662664;N:1022444	50	0	398259972	317724608	311519412	408662664	1022444	SRX11217414	SRS9271513	SRA1250059	GEO	Kaufman, Oncology, Washington University in St. Louis	1	0.89689		0.14892		0.73959		0.52927		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2021-06-24	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
65015	65015	SRR14902691	SRX11217413	SRS9271512	SRP325444	PRJNA741108	Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq]	GSE178801	Transcriptome Analysis	With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.	parent bioproject:PRJNA741103	pubmed:34791221	MA3A RNAseq	GSM5397958	source name:Sorted melanoma tumor\|genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma	MA3A RNAseq	Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as	Sorted melanoma tumor		FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit		genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma\|run #:1	GSM5397958	GSM5397958: MA3A RNAseq; Danio rerio; RNA Seq	GSM5397958		1	FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit	GEO Accession:GSM5397958	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP325444		MA3A.fq.gz	fastq	1442377200.0	28847544.0	GSM5397958 r1	0:50 1:0	A:405524842;C:314014451;G:304964281;T:416845768;N:1027858	50	0	405524842	314014451	304964281	416845768	1027858	SRX11217413	SRS9271512	SRA1250059	GEO	Kaufman, Oncology, Washington University in St. Louis	1	0.88956		0.1683		0.74018		0.52927		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2021-06-24	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
65016	65016	SRR14902690	SRX11217412	SRS9271511	SRP325444	PRJNA741108	Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq]	GSE178801	Transcriptome Analysis	With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.	parent bioproject:PRJNA741103	pubmed:34791221	MA2 RNAseq	GSM5397957	source name:Sorted melanoma tumor\|genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma	MA2 RNAseq	Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as	Sorted melanoma tumor		FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit		genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma\|run #:1	GSM5397957	GSM5397957: MA2 RNAseq; Danio rerio; RNA Seq	GSM5397957		1	FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit	GEO Accession:GSM5397957	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP325444		MA2.fq.gz	fastq	1402279300.0	28045586.0	GSM5397957 r1	0:50 1:0	A:389166788;C:306462364;G:298729361;T:406923403;N:997384	50	0	389166788	306462364	298729361	406923403	997384	SRX11217412	SRS9271511	SRA1250059	GEO	Kaufman, Oncology, Washington University in St. Louis	1	0.88844		0.14383		0.74923		0.53282		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2021-06-24	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
65017	65017	SRR14902689	SRX11217411	SRS9271510	SRP325444	PRJNA741108	Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq]	GSE178801	Transcriptome Analysis	With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.	parent bioproject:PRJNA741103	pubmed:34791221	MA1 RNAseq	GSM5397956	source name:Sorted melanoma tumor\|genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma	MA1 RNAseq	Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as	Sorted melanoma tumor		FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit		genotype:BRAFV600E/p53lf/lf/crestin:EGFP\|tissue:Melanoma\|run #:1	GSM5397956	GSM5397956: MA1 RNAseq; Danio rerio; RNA Seq	GSM5397956		1	FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit	GEO Accession:GSM5397956	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP325444		MA1.fq.gz	fastq	1456780700.0	29135614.0	GSM5397956 r1	0:50 1:0	A:403913103;C:308144749;G:305293739;T:438394612;N:1034497	50	0	403913103	308144749	305293739	438394612	1034497	SRX11217411	SRS9271510	SRA1250059	GEO	Kaufman, Oncology, Washington University in St. Louis	1	0.85833		0.16781		0.73407		0.52469		50		B		usable mapping rate	illumina	hiseq_era	full_length	cdna_unspecified	smarter	bulk	unknown	unknown	United States	2021-06-24	Undetermined	Adult	Cancer or Tumor	Cancer or Tumor
67037	67037	SRR17007607	SRX13197809	SRS11124869	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 6 S6: EVs3	GSM5699732	tissue:EVs3\|cell type:extracellular vesicles\|strain:kita:RAS	VA 6 S6: EVs3	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	EVs3		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:extracellular vesicles\|strain:kita:RAS	GSM5699732	GSM5699732: VA 6 S6: EVs3; Danio rerio; ncRNA Seq	GSM5699732 r1	GSM5699732	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_6_S6.fastq	fastq	1252482921.0	12400821.0	GSM5699732 r1	0:101	A:419008099;C:291188018;G:325856780;T:216362198;N:67826	101		419008099	291188018	325856780	216362198	67826	SRX13197809	SRS11124869	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.39065		0.05651		0.9752		0.82248		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
67038	67038	SRR17007608	SRX13197808	SRS11124868	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 5 S5: EVs2	GSM5699731	tissue:EVs2\|cell type:extracellular vesicles\|strain:kita:RAS	VA 5 S5: EVs2	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	EVs2		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:extracellular vesicles\|strain:kita:RAS	GSM5699731	GSM5699731: VA 5 S5: EVs2; Danio rerio; ncRNA Seq	GSM5699731 r1	GSM5699731	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_5_S5.fastq	fastq	1338062039.0	13248139.0	GSM5699731 r1	0:101	A:479478471;C:303639439;G:333339820;T:221533029;N:71280	101		479478471	303639439	333339820	221533029	71280	SRX13197808	SRS11124868	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.20158		0.0338		0.98979		0.73724		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
67039	67039	SRR17007609	SRX13197807	SRS11124867	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 4 S4: EVs1	GSM5699730	tissue:EVs1\|cell type:extracellular vesicles\|strain:kita:RAS	VA 4 S4: EVs1	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	EVs1		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:extracellular vesicles\|strain:kita:RAS	GSM5699730	GSM5699730: VA 4 S4: EVs1; Danio rerio; ncRNA Seq	GSM5699730 r1	GSM5699730	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_4_S4.fastq	fastq	1355391215.0	13419715.0	GSM5699730 r1	0:101	A:480538643;C:302531816;G:333018117;T:239227931;N:74708	101		480538643	302531816	333018117	239227931	74708	SRX13197807	SRS11124867	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.15363		0.03047		0.98563		0.85818		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
67040	67040	SRR17007610	SRX13197806	SRS11124866	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 24 S14: Melanoma3	GSM5699729	tissue:Melanoma3\|cell type:Melanocytes\|strain:kita:RAS	VA 24 S14: Melanoma3	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	Melanoma3		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:Melanocytes\|strain:kita:RAS	GSM5699729	GSM5699729: VA 24 S14: Melanoma3; Danio rerio; ncRNA Seq	GSM5699729 r1	GSM5699729	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_24_S14.fastq	fastq	1029043954.0	10188554.0	GSM5699729 r1	0:101	A:385266918;C:235984418;G:223100119;T:184638731;N:53768	101		385266918	235984418	223100119	184638731	53768	SRX13197806	SRS11124866	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.31444		0.04431		0.97477		0.79077		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
67041	67041	SRR17007611	SRX13197805	SRS11124865	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 23 S13: Melanoma2	GSM5699728	tissue:Melanoma2\|cell type:Melanocytes\|strain:kita:RAS	VA 23 S13: Melanoma2	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	Melanoma2		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:Melanocytes\|strain:kita:RAS	GSM5699728	GSM5699728: VA 23 S13: Melanoma2; Danio rerio; ncRNA Seq	GSM5699728 r1	GSM5699728	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_23_S13.fastq	fastq	1191776669.0	11799769.0	GSM5699728 r1	0:101	A:445740725;C:275311735;G:268819689;T:201841457;N:63063	101		445740725	275311735	268819689	201841457	63063	SRX13197805	SRS11124865	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.3168		0.04419		0.96978		0.837		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
67042	67042	SRR17007612	SRX13197804	SRS11124864	SRP347244	PRJNA782626	Characterization of zebrafish melanoma derived interstitial EVs and their ncRNA content	GSE189352	Transcriptome Analysis	Extracellular vesicles EVs are membranous particles released by all cell types. Their role as functional carriers of bioactive molecules is boosted in cancer where they can be either secreted in biological fluids or found in the intercellular space interstitial EVs iEVs. Here we have opti mised a method for the isolation and characterization of zebrafish iEVs from whole melanoma tissues. Zebrafish melanoma iEVs are in the range of 140 nm by nanoparticle tracking analysis NTA and TEM analysis. Western blot revealed enrichment for CD63 and Alix in the iEV frac tion but not in melanoma cell lysates. Super resolution and confocal microscopy revealed that purified zebrafish iEVs were GFP+ indicating that they integrate the oncogene GFP HRASV12G within their vesicular membrane. Analysis of RNA Seq data revealed that 118 ncRNAs are differentially distributed between zebrafish melanoma and their iEVs with only 18 of them be ing selectively enriched in iEVs. Among these the RNA components of RNAses MRP and P which process ribosomal RNA precursors mitochondrial RNAs and some mRNAs were enriched in iEVs. We found that melanoma iEVs induce an inflammatory response when injected in larval blood stream with increase of macrophage and induction of Interferon Responsive Genes. To clarify whether MRP and P contribute to the inflammation induced by melanoma iEVs we inject ed larvae with MRP or P RNAs and found an inflammatory response similar to that induced by melanoma iEVs. This suggests that zebrafish melanoma iEVs are a source of MRP and P RNAs that can trigger inflammation in cells of the tumor microenvironment. Overall design: In order to identify small RNAs preferentially accumulated in extracellular vesicles derived from zebrafish melanoma we performed RNA sequencing analysis RNA Seq of small RNAs isolated from EVs and melanoma samples.		pubmed:35628321	VA 22 S12: Melanoma1	GSM5699727	tissue:Melanoma1\|cell type:Melanocytes\|strain:Kita:RAS	VA 22 S12: Melanoma1	Basecalls performed using CASAVA Illumina Inc. Reads were aligned to the reference genome Danio rerio assembly GRCz11 using STAR [PMID: 23104886] with recommended options and thresholds version 2.5. HTSeq count version 0.9.1 [PMID: 25260700 ] was used to generate raw gene counts. EdgeR package version 3.24.3 [PMID: 19910308] was used to normalize counts to Trimmed Mean of M values TMM for visualization methods. Differential expression analysis was performed using DESeq2 package version 1.22.2 and for significance testing the Wald test was used. Genome build: GRCz11 Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	Melanoma1		RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.	Melanomas were induced in developing zebrafish through the Gal4/UAS system using the kita:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	cell type:Melanocytes\|strain:Kita:RAS	GSM5699727	GSM5699727: VA 22 S12: Melanoma1; Danio rerio; ncRNA Seq	GSM5699727 r1	GSM5699727	1	RNA extracts were collected from melanoma developing in adult zebrafish or from EVs isolated from the same tumors. Total RNA was isolated using Single Cell RNA Purification Kit Norgen following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Clontech SMARTer smRNA Seq kit. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.		ncRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2500	SRP347244	loader:fastq load.py	VA_22_S12.fastq	fastq	849183861.0	8407761.0	GSM5699727 r1	0:101	A:315648935;C:198401378;G:181384813;T:153698818;N:49917	101		315648935	198401378	181384813	153698818	49917	SRX13197804	SRS11124864	SRA1429699	Experimental Cancer Biology, CIBIO, University of Trento	Experimental Cancer Biology, CIBIO, University of Trento	1	0.37018		0.04901		0.96209		0.55085		101		B		usable mapping rate	illumina	hiseq_era	full_length	size_fractionation	smarter	bulk	unknown	unknown	Italy	2021-11-22	Adult	Adult	Cancer or Tumor	Cancer or Tumor
68974	68974	SRR18278274	SRX14416144	SRS12225423	SRP363191	PRJNA814235	Profiling the cancer prone microenvironment in a zebrafish model for MPNST	GSE198220	Transcriptome Analysis	Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low			Cancer Sox10 Low rep1	GSM5941038	source name:C Sox10 Low\|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1\|tissue:Cancer Microenvironment\|age:7.5 months\|treatment:Sox10 Low\|geo loc name:missing\|collection date:missing	Cancer Sox10 Low rep1	The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count	C Sox10 Low	Ocular tissues were removed enzymatically dissociated and processed by FACS	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended	Zebrafish housed and maintained under standard conditions	strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1\|tissue:Cancer Microenvironment\|age:7.5 months\|treatment:Sox10 Low	GSM5941038	GSM5941038: Cancer Sox10 Low rep1; Danio rerio; RNA Seq	GSM5941038 r1	GSM5941038	1	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP363191	loader:fastq load.py	OT2_RFPminus_S12_R1_001.fastq.gz OT2_RFPminus_S12_R2_001.fastq.gz	fastq fastq	7925709248.0	52142824.0	GSM5941038 r1	0:76 1:76	A:2103552320;C:1841208701;G:1890777758;T:2087293642;N:2876827	76	76	2103552320	1841208701	1890777758	2087293642	2876827	SRX14416144	SRS12225423	SRA1386032	Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University	CHHE, NCSU	2	0.92828	0.93268	0.12134	0.11797	0.72583	0.72823	0.52495	0.52004	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2022-03-09	Adult	Adult	Cancer or Tumor	Cancer or Tumor
68978	68978	SRR18278278	SRX14416140	SRS12225419	SRP363191	PRJNA814235	Profiling the cancer prone microenvironment in a zebrafish model for MPNST	GSE198220	Transcriptome Analysis	Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low			Cancer Sox10 High rep1	GSM5941034	source name:C Sox10 High\|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1\|tissue:Cancer Cells\|age:7.5 months\|treatment:Sox10 High\|geo loc name:missing\|collection date:missing	Cancer Sox10 High rep1	The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count	C Sox10 High	Ocular tissues were removed enzymatically dissociated and processed by FACS	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended	Zebrafish housed and maintained under standard conditions	strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1\|tissue:Cancer Cells\|age:7.5 months\|treatment:Sox10 High	GSM5941034	GSM5941034: Cancer Sox10 High rep1; Danio rerio; RNA Seq	GSM5941034 r1	GSM5941034	1	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500	SRP363191	loader:fastq load.py	OT2_RFPplus_S13_R1_001.fastq.gz OT2_RFPplus_S13_R2_001.fastq.gz	fastq fastq	8467944472.0	55710161.0	GSM5941034 r1	0:76 1:76	A:2301977921;C:1929368914;G:1962397726;T:2271138508;N:3061403	76	76	2301977921	1929368914	1962397726	2271138508	3061403	SRX14416140	SRS12225419	SRA1386032	Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University	CHHE, NCSU	2	0.92478	0.9291	0.17477	0.17197	0.74574	0.74692	0.54039	0.53058	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown	United States	2022-03-09	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74560	74560	SRR23829118	SRX19650818	SRS17019470	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/10	7B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep4\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	7B	7B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		7B_1.fq.gz 7B_2.fq.gz	fastq fastq	10796340200.0	53981701.0	7B 1.fq.gz	0:100 1:100	A:2946489343;C:2411825502;G:2477056291;T:2960969064;N:0	100	100	2946489343	2411825502	2477056291	2960969064	0	SRX19650818	SRS17019470	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91639	0.92098	0.13624	0.1358	0.7443	0.74367	0.52593	0.52158	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74561	74561	SRR23829119	SRX19650817	SRS17019469	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/12	8B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	8B	8B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		8B_1.fq.gz 8B_2.fq.gz	fastq fastq	10560562800.0	52802814.0	8B 1.fq.gz	0:100 1:100	A:2867789187;C:2366678430;G:2438457525;T:2887637658;N:0	100	100	2867789187	2366678430	2438457525	2887637658	0	SRX19650817	SRS17019469	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.90976	0.91391	0.15248	0.15201	0.73499	0.73379	0.51572	0.51882	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74562	74562	SRR23829120	SRX19650816	SRS17019468	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2806/1	9B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:28.06.2021\|genotype:tert / rep4\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	9B	9B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		9B_1.fq.gz 9B_2.fq.gz	fastq fastq	10805598600.0	54027993.0	9B 1.fq.gz	0:100 1:100	A:2899169569;C:2457980147;G:2528851393;T:2919597491;N:0	100	100	2899169569	2457980147	2528851393	2919597491	0	SRX19650816	SRS17019468	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92637	0.93052	0.12486	0.12507	0.73352	0.73188	0.51498	0.52101	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74563	74563	SRR23829121	SRX19650815	SRS17019467	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2806/2	10B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:28.06.2021\|genotype:tert+/+ rep1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	10B	10B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		10B_1.fq.gz 10B_2.fq.gz	fastq fastq	10811556000.0	54057780.0	10B 1.fq.gz	0:100 1:100	A:2898576858;C:2460872365;G:2527128196;T:2924978581;N:0	100	100	2898576858	2460872365	2527128196	2924978581	0	SRX19650815	SRS17019467	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92176	0.92836	0.12295	0.12256	0.72604	0.72458	0.51306	0.51966	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74564	74564	SRR23829122	SRX19650814	SRS17019466	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/9	6B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	6B	6B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		6B_1.fq.gz 6B_2.fq.gz	fastq fastq	10809952000.0	54049760.0	6B 1.fq.gz	0:100 1:100	A:2931041183;C:2429723251;G:2502283305;T:2946904261;N:0	100	100	2931041183	2429723251	2502283305	2946904261	0	SRX19650814	SRS17019466	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92179	0.92775	0.13661	0.1365	0.74679	0.74556	0.52477	0.52471	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74565	74565	SRR23829123	SRX19650813	SRS17019465	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/8	5B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	5B	5B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		5B_1.fq.gz 5B_2.fq.gz	fastq fastq	10604822000.0	53024110.0	5B 1.fq.gz	0:100 1:100	A:2847359136;C:2411906169;G:2481911629;T:2863645066;N:0	100	100	2847359136	2411906169	2481911629	2863645066	0	SRX19650813	SRS17019465	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92231	0.92771	0.13302	0.13258	0.74052	0.73843	0.51718	0.51163	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74566	74566	SRR23829124	SRX19650812	SRS17019464	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/7	4B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	4B	4B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		4B_1.fq.gz 4B_2.fq.gz	fastq fastq	10792140600.0	53960703.0	4B 1.fq.gz	0:100 1:100	A:2882693797;C:2464129073;G:2535344124;T:2909973606;N:0	100	100	2882693797	2464129073	2535344124	2909973606	0	SRX19650812	SRS17019464	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91884	0.92345	0.12967	0.12884	0.74117	0.74103	0.50792	0.51065	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74567	74567	SRR23829125	SRX19650811	SRS17019463	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/4	3B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert / rep3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	3B	3B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		3B_1.fq.gz 3B_2.fq.gz	fastq fastq	10817072400.0	54085362.0	3B 1.fq.gz	0:100 1:100	A:2980754877;C:2390812269;G:2448674730;T:2996830524;N:0	100	100	2980754877	2390812269	2448674730	2996830524	0	SRX19650811	SRS17019463	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91015	0.9166	0.15854	0.15694	0.73724	0.73442	0.5243	0.52496	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74568	74568	SRR23829126	SRX19650810	SRS17019462	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2104/14	19B	strain:AB\|age:10 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:21.04.2021\|genotype:tert / rep3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 10 month male tumor	19B	19B	RNA Seq of Danio rerio : 10 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		19B_1.fq.gz 19B_2.fq.gz	fastq fastq	12603676000.0	63018380.0	19B 1.fq.gz	0:100 1:100	A:3414935292;C:2859787251;G:2916851430;T:3412102027;N:0	100	100	3414935292	2859787251	2916851430	3412102027	0	SRX19650810	SRS17019462	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92494	0.92995	0.12064	0.12054	0.73807	0.73649	0.52554	0.52564	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74569	74569	SRR23829127	SRX19650809	SRS17019461	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2104/9	18B	strain:AB\|age:10 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:21.04.2021\|genotype:tert / rep2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 10 month male tumor	18B	18B	RNA Seq of Danio rerio : 10 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		18B_1.fq.gz 18B_2.fq.gz	fastq fastq	12562625800.0	62813129.0	18B 1.fq.gz	0:100 1:100	A:3435125429;C:2818006678;G:2880078673;T:3429415020;N:0	100	100	3435125429	2818006678	2880078673	3429415020	0	SRX19650809	SRS17019461	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92476	0.92851	0.12505	0.12384	0.74961	0.74882	0.52843	0.52817	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74570	74570	SRR23829128	SRX19650808	SRS17019460	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2104/1	17B	strain:AB\|age:10 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:21.04.2021\|genotype:tert+/+ rep5\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 10 month male tumor	17B	17B	RNA Seq of Danio rerio : 10 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		17B_1.fq.gz 17B_2.fq.gz	fastq fastq	8787148400.0	43935742.0	17B 1.fq.gz	0:100 1:100	A:2617726378;C:1773416208;G:1829194025;T:2566811789;N:0	100	100	2617726378	1773416208	1829194025	2566811789	0	SRX19650808	SRS17019460	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.84629	0.85164	0.49471	0.49585	0.79545	0.79275	0.64785	0.57659	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74571	74571	SRR23829129	SRX19650807	SRS17019459	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2806/3	16B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:28.06.2021\|genotype:tert+/+ rep4\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	16B	16B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		16B_1.fq.gz 16B_2.fq.gz	fastq fastq	12372317000.0	61861585.0	16B 1.fq.gz	0:100 1:100	A:3325923130;C:2824746317;G:2889873754;T:3331773799;N:0	100	100	3325923130	2824746317	2889873754	3331773799	0	SRX19650807	SRS17019459	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92023	0.92579	0.13379	0.13406	0.75974	0.75954	0.51721	0.53155	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74572	74572	SRR23829130	SRX19650806	SRS17019458	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2506/2	15B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:25.06.2021\|genotype:tert+/+ rep3\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	15B	15B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		15B_1.fq.gz 15B_2.fq.gz	fastq fastq	12111580000.0	60557900.0	15B 1.fq.gz	0:100 1:100	A:3253473957;C:2781714853;G:2829572138;T:3246819052;N:0	100	100	3253473957	2781714853	2829572138	3246819052	0	SRX19650806	SRS17019458	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92909	0.9333	0.12994	0.13008	0.76997	0.76921	0.53473	0.52603	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74573	74573	SRR23829131	SRX19650805	SRS17019457	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2506/1	14B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:25.06.2021\|genotype:tert / rep1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	14B	14B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		14B_1.fq.gz 14B_2.fq.gz	fastq fastq	12314492000.0	61572460.0	14B 1.fq.gz	0:100 1:100	A:3364570176;C:2760126284;G:2813170851;T:3376624689;N:0	100	100	3364570176	2760126284	2813170851	3376624689	0	SRX19650805	SRS17019457	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.92824	0.93249	0.16314	0.16227	0.74217	0.74142	0.54103	0.54082	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74574	74574	SRR23829132	SRX19650804	SRS17019456	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/11	13B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert+/+ rep6\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	13B	13B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		13B_1.fq.gz 13B_2.fq.gz	fastq fastq	12281192200.0	61405961.0	13B 1.fq.gz	0:100 1:100	A:3369650885;C:2745871807;G:2821246280;T:3344423228;N:0	100	100	3369650885	2745871807	2821246280	3344423228	0	SRX19650804	SRS17019456	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.93143	0.93303	0.1814	0.18252	0.76207	0.76169	0.55108	0.54553	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74575	74575	SRR23829133	SRX19650803	SRS17019455	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/2	12B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert / rep4\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	12B	12B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		12B_1.fq.gz 12B_2.fq.gz	fastq fastq	12163842800.0	60819214.0	12B 1.fq.gz	0:100 1:100	A:3431206764;C:2629189354;G:2672190281;T:3431256401;N:0	100	100	3431206764	2629189354	2672190281	3431256401	0	SRX19650803	SRS17019455	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91204	0.91933	0.22594	0.22625	0.73777	0.73586	0.5046	0.47081	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74576	74576	SRR23829134	SRX19650802	SRS17019454	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			2806/4	11B	strain:AB\|age:12 month\|sex:male\|tissue:Tumor\|birth date:24.06.2020\|birth location:PEMAV IRCAN France\|death date:28.06.2021\|genotype:tert+/+ rep2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 12 month male tumor	11B	11B	RNA Seq of Danio rerio : 12 month male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		11B_1.fq.gz 11B_2.fq.gz	fastq fastq	10583058000.0	52915290.0	11B 1.fq.gz	0:100 1:100	A:2970647072;C:2293859072;G:2357521919;T:2961029937;N:0	100	100	2970647072	2293859072	2357521919	2961029937	0	SRX19650802	SRS17019454	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.90787	0.91228	0.1916	0.19016	0.72271	0.72092	0.52084	0.52228	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74577	74577	SRR23829135	SRX19650801	SRS17019453	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/3	2B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert / rep2\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	2B	2B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		2B_1.fq.gz 2B_2.fq.gz	fastq fastq	10776715000.0	53883575.0	2B 1.fq.gz	0:100 1:100	A:2948670507;C:2400698003;G:2461964006;T:2965382484;N:0	100	100	2948670507	2400698003	2461964006	2965382484	0	SRX19650801	SRS17019453	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91594	0.91925	0.17372	0.17392	0.73708	0.73742	0.52748	0.53599	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	Cancer or Tumor	Cancer or Tumor
74578	74578	SRR23829136	SRX19650800	SRS17019452	SRP426991	PRJNA944150	Absence of telomerase restricts melanoma development.	PRJNA944150	Other	Most cancers reactivate telomerase to maintain telomere length to acquire immortality. The importance of this process is well illustrated by the fact that telomerase promoter mutations are found at a high frequency in many cancer types including melanoma. However it is unclear when and if telomerase is strictly required during tumorigenesis. Here we show that melanoma can occur in the absence of telomerase. Nevertheless it is required to sustain later growth and avoid regression. Using telomerase mutant zebrafish tert / combined with two established melanoma models we found equal melanoma incidence and invasiveness as tumors became visible. Later however while WT fish develop increasing larger tumors tert / tumors stagnate growth and regress. Consistently tert / tumors showed lower cell proliferation higher apoptosis and melanocyte differentiation. We also detected an immune response to tert / tumors. Indeed tert / tumors resumed growth when transplanted to immunocompromised hosts. We propose that telomerase is required for melanoma in zebrafish albeit at later stages of progression to sustain growth while avoiding immune rejection and regression. Thus absence of telomerase restricts melanoma through tumor autonomous mechanisms cell cycle arrest apoptosis and melanocyte differentiation and a non tumor autonomous mechanisms immune rejection.			3006/1	1B	strain:AB\|age:3 month\|sex:male\|tissue:Tumor\|birth date:10.03.2021\|birth location:PEMAV IRCAN France\|death date:30.06.2021\|genotype:tert / rep1\|BioSampleModel:Model organism or animal									RNA Seq of Danio rerio : 3months male tumor	1B	1B	RNA Seq of Danio rerio : 3months male tumor			RNA-Seq	TRANSCRIPTOMIC	Oligo-dT	PAIRED	BGISEQ	BGISEQ-500	SRP426991		1B_1.fq.gz 1B_2.fq.gz	fastq fastq	10556248400.0	52781242.0	1B 1.fq.gz	0:100 1:100	A:2849865226;C:2384848330;G:2457353526;T:2864181318;N:0	100	100	2849865226	2384848330	2457353526	2864181318	0	SRX19650800	SRS17019452	SRA1603485	Sun Yat-sen University Cancer Center\|State Key Laboratory of Oncology in South China	Sun Yat-sen University Cancer Center Miguel Godinho Ferreira	2	0.91378	0.91775	0.13203	0.13044	0.73373	0.73342	0.51084	0.51194	100	100	B	B	biological fallback assumption	bgi	bgi	unknown	poly_a	unknown	bulk	unknown	unknown	China	2023-03-14	Adult	Adult	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");;