{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Adult\" and tissue_curation_coarse = \"Cancer or Tumor\"", "rows": [[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. 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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", null, "ZF melanoma rep2", "GSM2199907", null, "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", null, "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", null, "1", "RNA was harvested from cells using Trizol reagent. 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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", null, "ZF melanoma rep1", "GSM2199906", null, "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", null, "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", null, "1", "RNA was harvested from cells using Trizol reagent. Illumina TruSeq", "GEO Accession:GSM2199906", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP076552", null, null, "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, null, null, 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", null, "United States", "2016-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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", null, "pubmed:28903419", null, "FFPE 2", "GSM2424730", null, "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", null, "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.", null, "strain:p53M214K|tissue:tumor tissues 2 induced by rb1 TALENs|developmental stage:5 mpf", "GSM2424730", "GSM2424730: FFPE 2; Danio rerio; RNA Seq", "GSM2424730", null, "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", null, "SRP094947", null, null, "FFPE-2_fastq.gz", "fastq", 900420050.0, 8915050.0, "GSM2424730 r1", "0:101", "A:404381931;C:201118712;G:149335807;T:145550067;N:33533", 101, null, null, null, 404381931, 201118712, 149335807, 145550067, 33533, "SRX2415891", "SRS1853479", "SRA502460", "GEO", "Research Institute, National Cancer Center", 1, 0.03639, null, 0.02825, null, 0.9978, null, 0.55688, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2016-12-12", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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", null, "pubmed:28903419", null, "FFPE 1", "GSM2424729", null, "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", null, "RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. 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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", null, "SRP094947", null, null, "FFPE-1_fastq.gz", "fastq", 985654556.0, 9758956.0, "GSM2424729 r1", "0:101", "A:642158389;C:109642019;G:103170689;T:130633868;N:49591", 101, null, null, null, 642158389, 109642019, 103170689, 130633868, 49591, "SRX2415890", "SRS1853478", "SRA502460", "GEO", "Research Institute, National Cancer Center", 1, 0.71847, null, 0.59813, null, 0.9376, null, 0.57167, null, 101, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2016-12-12", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Nuc seq", "GSM5380072", null, "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", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. Droplet based snRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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\u2019s instructions.\u00a0", null, "sample type:Single nucleus suspension", "GSM5380072", "GSM5380072: Nuc seq; Danio rerio; RNA Seq", "GSM5380072", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. 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", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2021-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Nuc seq", "GSM5380072", null, "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", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. Droplet based snRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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\u2019s instructions.\u00a0", null, "sample type:Single nucleus suspension", "GSM5380072", "GSM5380072: Nuc seq; Danio rerio; RNA Seq", "GSM5380072", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. 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", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2021-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Nuc seq", "GSM5380072", null, "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", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. Droplet based snRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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\u2019s instructions.\u00a0", null, "sample type:Single nucleus suspension", "GSM5380072", "GSM5380072: Nuc seq; Danio rerio; RNA Seq", "GSM5380072", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. 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", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2021-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Nuc seq", "GSM5380072", null, "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", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. Droplet based snRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 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\u2019s instructions.\u00a0", null, "sample type:Single nucleus suspension", "GSM5380072", "GSM5380072: Nuc seq; Danio rerio; RNA Seq", "GSM5380072", null, "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\u00b0C 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/\u00b5L RNAse inhibitor  the sample was again spun at 4\u00b0C for 5 min at 500g. The pellet was resuspended in 1 mL wash buffer and subsequently sorted at 4\u00b0C 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\u00b0C. 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", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2021-06-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "SingleCell F", "GSM4838135", null, "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", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3\u2019 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 \u00b5m 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.\u00a0 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics 3\u2019 GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 Chip G 10X Genomics. Approximately 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer\u2019s instructions.", null, "sample type:Single cell suspension", "GSM4838135", "GSM4838135: SingleCell F; Danio rerio; RNA Seq", "GSM4838135", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C 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 \u00b5m 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA 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 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.", "GEO Accession:GSM4838135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2020-10-20", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "SingleCell E", "GSM4838134", null, "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", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3\u2019 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 \u00b5m 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.\u00a0 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics 3\u2019 GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 Chip G 10X Genomics. Approximately 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer\u2019s instructions.", null, "sample type:Single cell suspension", "GSM4838134", "GSM4838134: SingleCell E; Danio rerio; RNA Seq", "GSM4838134", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C 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 \u00b5m 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA 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 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.", "GEO Accession:GSM4838134", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2020-10-20", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Visium C", "GSM4838133", null, "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", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3\u2019 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 \u00b5m 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.\u00a0 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics 3\u2019 GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 Chip G 10X Genomics. Approximately 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer\u2019s instructions.", null, "sample type:Tissue cryosections", "GSM4838133", "GSM4838133: Visium C; Danio rerio; RNA Seq", "GSM4838133", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C 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 \u00b5m 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA 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 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.", "GEO Accession:GSM4838133", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2020-10-20", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Visium B", "GSM4838132", null, "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", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3\u2019 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 \u00b5m 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.\u00a0 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics 3\u2019 GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 Chip G 10X Genomics. Approximately 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer\u2019s instructions.", null, "sample type:Tissue cryosections", "GSM4838132", "GSM4838132: Visium B; Danio rerio; RNA Seq", "GSM4838132", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C 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 \u00b5m 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA 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 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.", "GEO Accession:GSM4838132", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2020-10-20", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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 \u201cinterface\u201d 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 such zebrafish pooled into one reaction.", null, "pubmed:34725363", null, "Visium A", "GSM4838131", null, "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", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C for a maximum of one week before use. For single cell RNA seq using the 10X genomics 3\u2019 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 \u00b5m 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.\u00a0 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics 3\u2019 GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA seq was performed using the Chromium Single Cell 3\u2019 Library & Gel Bead Kit v3 10X Genomics and Chromium Single Cell 3\u2019 Chip G 10X Genomics. Approximately 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer\u2019s instructions.", null, "sample type:Tissue cryosections", "GSM4838131", "GSM4838131: Visium A; Danio rerio; RNA Seq", "GSM4838131", null, "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\u00b0C. For cryosectioning  both the tissue block and the ST slide were equilibrated inside the cryostat for 15 30 minutes at 16\u00b0C before sectioning. Transverse sections through the entire fish were cut at a thickness of 10 \u00b5m and immediately placed on the ST slide Visium Spatial Gene Expression Slides  10X Genomics. ST slides containing sections were stored at  80\u00b0C 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 \u00b5m 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\u00b0C  stained with hematoxylin and eosin  and mounted in 85% glycerol for imaging. Imaging was performed on a Leica SCN400 F whole slide scanner at 40X magnification. post imaging  sections were permeabilized at 37\u00b0C for 45 minutes. post permeabilization  the on slide reverse transcription RT reaction was performed at 53\u00b0C for 2 hours. Permeabilization time and RT reaction length were determined using the Visium Spatial Tissue Optimization Kit 10X Genomics. Second strand synthesis was subsequently performed on slide for 15 minutes at 65\u00b0C. All on slide reactions were performed in a thermocycler with a metal slide adaptor plate. Following second strand synthesis  samples were transferred to tubes for cDNA amplification and cleanup. Library quality was assayed using a Bioanalyzer High Sensitivity chip Agilent. For single cell RNA seq using the 10X genomics three prime GEX v3 platform: Equal numbers of sorted GFP+ tumor and GFP  macroenvironment cells were centrifuged at 300g for 5 minutes at RT  and resuspended in DMEM + 10% FBS. Droplet based scRNA 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 10 000 cells from two fish were split encapsulated in a single v3 reaction. GEM generation and library preparation were performed according to manufacturer's instructions.", "GEO Accession:GSM4838131", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP287858", null, null, "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, null, null, 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", null, "United States", "2020-10-20", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 6 S6: EVs3", "GSM5699732", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.05651, null, 0.9752, null, 0.82248, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 5 S5: EVs2", "GSM5699731", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.0338, null, 0.98979, null, 0.73724, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 4 S4: EVs1", "GSM5699730", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.03047, null, 0.98563, null, 0.85818, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 24 S14: Melanoma3", "GSM5699729", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.04431, null, 0.97477, null, 0.79077, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 23 S13: Melanoma2", "GSM5699728", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.04419, null, 0.96978, null, 0.837, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, "pubmed:35628321", null, "VA 22 S12: Melanoma1", "GSM5699727", null, "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", null, "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\u2019s 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.", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP347244", null, "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, null, null, null, 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, null, 0.04901, null, 0.96209, null, 0.55085, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "full_length", "size_fractionation", "smarter", "bulk", "unknown", "unknown", null, "Italy", "2021-11-22", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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", null, null, null, "Cancer Sox10 Low  rep1", "GSM5941038", null, "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\u2019 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\u00a0counts 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\u00a0 gene symbol and summed.\u00a0DESeq2 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP363191", null, "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, null, null, 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", null, "United States", "2022-03-09", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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", null, null, null, "Cancer Sox10 High  rep1", "GSM5941034", null, "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\u2019 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\u00a0counts 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\u00a0 gene symbol and summed.\u00a0DESeq2 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP363191", null, "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, null, null, 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", null, "United States", "2022-03-09", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/10", "7B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "7B", "7B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/12", "8B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "8B", "8B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2806/1", "9B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "9B", "9B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2806/2", "10B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "10B", "10B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/9", "6B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "6B", "6B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/8", "5B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "5B", "5B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/7", "4B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "4B", "4B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/4", "3B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "3B", "3B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2104/14", "19B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 10 month male tumor", "19B", "19B", "RNA Seq of Danio rerio : 10 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2104/9", "18B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 10 month male tumor", "18B", "18B", "RNA Seq of Danio rerio : 10 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2104/1", "17B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 10 month male tumor", "17B", "17B", "RNA Seq of Danio rerio : 10 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2806/3", "16B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "16B", "16B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2506/2", "15B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "15B", "15B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2506/1", "14B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "14B", "14B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/11", "13B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "13B", "13B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/2", "12B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "12B", "12B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "2806/4", "11B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 12 month male tumor", "11B", "11B", "RNA Seq of Danio rerio : 12 month male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/3", "2B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "2B", "2B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"], [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.", null, null, null, "3006/1", "1B", null, "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", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio : 3months male tumor", "1B", "1B", "RNA Seq of Danio rerio : 3months male tumor", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP426991", null, null, "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, null, null, 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", null, "China", "2023-03-14", "Adult", "Adult", "Cancer or Tumor", "Cancer or Tumor"]], "truncated": false, "filtered_table_rows_count": 42, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "Adult", "p1": "Cancer or Tumor"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": 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