{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Undetermined\" and tissue_curation = \"Skin\"", "rows": [[33894, "SRR30866028", "SRX26263941", "SRS22803195", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "m4b mut melanoma  biol rep 2", "GSM8552314", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing", "m4b mut melanoma  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI", "GSM8552314", "GSM8552314: m4b mut melanoma  biol rep 2; Danio rerio; RNA Seq", "GSM8552314 r1", "GSM8552314", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "MKO2_S39_R1_001.fastq.gz MKO2_S39_R2_001.fastq.gz", "fastq fastq", 3705364625.0, 14164066.0, "GSM8552314 r1", "0:126.72 1:134.89", "A:785806700;C:949078797;G:1178279032;T:784972987;N:7227109", 126, 134, null, null, 785806700, 949078797, 1178279032, 784972987, 7227109, "SRX26263941", "SRS22803195", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33895, "SRR30866029", "SRX26263940", "SRS22803194", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "m4b mut melanoma  biol rep 1", "GSM8552313", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI|geo loc name:missing|collection date:missing", "m4b mut melanoma  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:mgat4b mutant|treatment:MAZERATI", "GSM8552313", "GSM8552313: m4b mut melanoma  biol rep 1; Danio rerio; RNA Seq", "GSM8552313 r1", "GSM8552313", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "MKO1_S38_R1_001.fastq.gz MKO1_S38_R2_001.fastq.gz", "fastq fastq", 4779377372.0, 18058294.0, "GSM8552313 r1", "0:128.72 1:135.94", "A:1016908920;C:1236613888;G:1502465334;T:1018053808;N:5335422", 128, 135, null, null, 1016908920, 1236613888, 1502465334, 1018053808, 5335422, "SRX26263940", "SRS22803194", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33896, "SRR30866030", "SRX26263939", "SRS22803193", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "wild type melanoma control  biol rep 2", "GSM8552312", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing", "wild type melanoma control  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI", "GSM8552312", "GSM8552312: wild type melanoma control  biol rep 2; Danio rerio; RNA Seq", "GSM8552312 r1", "GSM8552312", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "EV2_S37_R1_001.fastq.gz EV2_S37_R2_001.fastq.gz", "fastq fastq", 5427379509.0, 19981504.0, "GSM8552312 r1", "0:133.16 1:138.46", "A:1136639418;C:1414638483;G:1736492639;T:1137614638;N:1994331", 133, 138, null, null, 1136639418, 1414638483, 1736492639, 1137614638, 1994331, "SRX26263939", "SRS22803193", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33897, "SRR30866031", "SRX26263938", "SRS22803192", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "wild type melanoma control  biol rep 1", "GSM8552311", null, "source name:skin|tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI|geo loc name:missing|collection date:missing", "wild type melanoma control  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanoma|genotype:WT|treatment:MAZERATI", "GSM8552311", "GSM8552311: wild type melanoma control  biol rep 1; Danio rerio; RNA Seq", "GSM8552311 r1", "GSM8552311", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "EV1_S36_R1_001.fastq.gz EV1_S36_R2_001.fastq.gz", "fastq fastq", 5248108957.0, 19087024.0, "GSM8552311 r1", "0:135.12 1:139.84", "A:1112163842;C:1354895660;G:1658732932;T:1120342985;N:1973538", 135, 139, null, null, 1112163842, 1354895660, 1658732932, 1120342985, 1973538, "SRX26263938", "SRS22803192", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33898, "SRR30866032", "SRX26263937", "SRS22803191", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "melanophore  biol rep 2", "GSM8552310", null, "source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing", "melanophore  biol rep 2", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanophore|genotype:WT|treatment:No", "GSM8552310", "GSM8552310: melanophore  biol rep 2; Danio rerio; RNA Seq", "GSM8552310 r1", "GSM8552310", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "WT2_S41_R1_001.fastq.gz WT2_S41_R2_001.fastq.gz", "fastq fastq", 4636631881.0, 16340506.0, "GSM8552310 r1", "0:140.47 1:143.28", "A:1114533149;C:1104066636;G:1293649625;T:1122672029;N:1710442", 140, 143, null, null, 1114533149, 1104066636, 1293649625, 1122672029, 1710442, "SRX26263937", "SRS22803191", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [33899, "SRR30866033", "SRX26263936", "SRS22803190", "SRP536275", "PRJNA1168148", "Mgat4b mediated selective N glycosyl modification regulates melanocyte development and melanoma progression [bulk RNA seq]", "GSE278653", "Transcriptome Analysis", "Dysregulated melanocyte state transitions are a pivotal driver of melanoma development  highlighting the need to identify key regulators of these processes. Understanding these factors is key to know how normal melanocyte functions and shift towards initiation of melanoma. Our study identifies Mgat4b  a glycosyl transferase involved in selective N glycan branching enriched in pigment progenitors  as a key regulator of directional melanocyte migration and establishment of Melanocyte stem cell McSC pool during early development in zebrafish and mammalian melanocytes. Single cell RNA sequencing analysis in zebrafish upon targeted disruption of Mgat4b reveals that a subset of melanocytes marked by aberrant galectin expression are impaired in migration and are lost. Lectin binding proteomic analysis reveals the glycosylation of key melanocyte proteins Gpnmb  Kit  and Tyrp1 to be under the control of Mgat4b. Additionally  mislocalization of Gamma catenin Jup explains the observed defects in cell adhesion and migration to be regulated by mgat4b but not its isozyme mgat4a. Our meta analysis further revealed that melanoma patients with both the BrafV600E mutation and elevated Mgat4b levels have significantly worse survival outcomes compared to those with only the BrafV600E mutation. By leveraging the MAZERATI platform to model BrafV600E driver mutation in vivo  we show that Mgat4b mutant cells fail to aggregate and initiate tumors. Our study underscores the importance of selective N glycan branching in both melanocyte development and melanoma initiation  suggesting a Mitf controlled Mgat4b as a promising therapeutic target for melanoma treatment. Overall design: To investigate the mechanisms that inhibit mutant cells from initiating melanoma in the absence of mgat4b  we utilized mature melanophores and melanoma cells from the skin of five zebrafish  including both MAZERATI wild type and  MAZERATI zebrafish carrying mgat4b mutations. We then performed gene expression profiling analysis using data obtained from RNA seq of melanophores and melanoma cells from both the zebrafish wild type and m4b mut. Comparative gene expression analysis was performed for wild type melanoma and melanophores  m4b mut melanoma and melanophores  wild type and m4b mut melanoma.", null, null, null, "melanophore  biol rep 1", "GSM8552309", null, "source name:skin|tissue:skin|cell type:melanophore|genotype:WT|treatment:No|geo loc name:missing|collection date:missing", "melanophore  biol rep 1", "Raw fastq files were trimmed using trimmomatic to remove adaptors and retain high quality reads. The reads were then aligned with zebrafish reference assembly GRCz11 using STAR. Featurecounts was used to calculate raw counts from the aligned reads. Assembly: GRCz11 Supplementary files format and content: tab delimited text file including raw counts for each sample", "skin", null, "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "tissue:skin|cell type:melanophore|genotype:WT|treatment:No", "GSM8552309", "GSM8552309: melanophore  biol rep 1; Danio rerio; RNA Seq", "GSM8552309 r1", "GSM8552309", "1", "The cell isolation process involved density gradient centrifugation  followed by RNA extraction using Trizol method. Illumina standard total RNA prep kit was used for library construction", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP536275", null, null, "WT1_S40_R1_001.fastq.gz WT1_S40_R2_001.fastq.gz", "fastq fastq", 5185761246.0, 18118534.0, "GSM8552309 r1", "0:141.81 1:144.40", "A:1231235669;C:1235759770;G:1476864583;T:1240636871;N:1264353", 141, 144, null, null, 1231235669, 1235759770, 1476864583, 1240636871, 1264353, "SRX26263936", "SRS22803190", "SRA1984938", "Pigment Cell Biology Lab, CSIR-IGIB", "Pigment Cell Biology Lab, CSIR-IGIB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "trueseq", "sc_generic", "bulk", "bulk", null, "India", "2024-10-02", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [63898, "SRR14213368", "SRX10579913", "SRS8684381", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Skin3", "GSM5237137", null, "source name:zebrafish skin|genotype:wild type|tissue:skin|strain:TLAB", "Skin3", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish skin", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:skin|strain:TLAB", "GSM5237137", "GSM5237137: Skin3; Danio rerio; RNA Seq", "GSM5237137", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237137", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Skin3.fastq", "fastq", 1791301700.0, 17913017.0, "GSM5237137 r1", "0:100", "A:461644132;C:423476905;G:420663755;T:485448242;N:68666", 100, null, null, null, 461644132, 423476905, 420663755, 485448242, 68666, "SRX10579913", "SRS8684381", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95551, null, 0.07734, null, 0.76828, null, 0.55723, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [63899, "SRR14213394", "SRX10579912", "SRS8684380", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Skin2", "GSM5237136", null, "source name:zebrafish skin|genotype:wild type|tissue:skin|strain:TLAB", "Skin2", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish skin", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:skin|strain:TLAB", "GSM5237136", "GSM5237136: Skin2; Danio rerio; RNA Seq", "GSM5237136", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237136", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Skin2.fastq", "fastq", 1540878000.0, 15408780.0, "GSM5237136 r1", "0:100", "A:394401295;C:368888243;G:364934471;T:412595940;N:58051", 100, null, null, null, 394401295, 368888243, 364934471, 412595940, 58051, "SRX10579912", "SRS8684380", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.94678, null, 0.09904, null, 0.75306, null, 0.54337, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [63900, "SRR14213393", "SRX10579911", "SRS8684379", "SRP314470", "PRJNA721381", "RNA Seq from zebrafish adult tissues", "GSE171906", "Transcriptome Analysis", "The goal of this study was to profile transcript expression levels across zebrafish adult tissues. Overall design: Transcriptome profiles of nine zebrafish adult tissues. Every tissue contains triplicates.", null, "pubmed:34556579", null, "Skin1", "GSM5237135", null, "source name:zebrafish skin|genotype:wild type|tissue:skin|strain:TLAB", "Skin1", "Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode BAM files containing sequencing reads were converted to fastq files using samtools v1.9 Barcoded libraries were demultiplexed using fastx toolkit v0.0.14 Sequencing adapters were trimmed with cutadapt v1.18 and only reads longer than 25 bases were kept Reads were aligned to GRCz11 with Hisat2 v2.1.0  using the Ensembl transcriptome release 102. The following parameters were used: hisat2  q   dta   rna strandness R  k 12   no unal Quantification at the gene level to obtain transcript per million TPM was perfomed using Kallisto v0.43.0 Genome build: GRCz11 Supplementary files format and content: Tab delimited files containing TPM", "zebrafish skin", null, "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "Zebrafish Danio rerio were raised according to standard protocols 28\u00b0C water temperature; 14/10 hour light/dark cycle", "genotype:wild type|tissue:skin|strain:TLAB", "GSM5237135", "GSM5237135: Skin1; Danio rerio; RNA Seq", "GSM5237135", null, "1", "Total RNA was extracted using the standard TRIzol Invitrogen protocol. To obtain polyA+ RNA  the polyA selection kit from LEXOGEN was used. Strand specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina", "GEO Accession:GSM5237135", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP314470", null, null, "Skin1.fastq", "fastq", 1894948100.0, 18949481.0, "GSM5237135 r1", "0:100", "A:486879091;C:450700393;G:453217896;T:504078083;N:72637", 100, null, null, null, 486879091, 450700393, 453217896, 504078083, 72637, "SRX10579911", "SRS8684379", "SRA1217576", "GEO", "Pauli lab, Research Institute of Molecular Pathology", 1, 0.95498, null, 0.07021, null, 0.75986, null, 0.55816, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2021-04-12", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69552, "SRR18901596", "SRX14979865", "SRS12729755", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgDGAT1a 3 bulk RNAseq", "GSM6062270", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "sgDGAT1a 3 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "GSM6062270", "GSM6062270: sgDGAT1a 3 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062270 r1", "GSM6062270", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "DGAT1a_3_R1.fastq.gz DGAT1a_3_R2.fastq.gz", "fastq fastq", 6999632088.0, 34651644.0, "GSM6062270 r1", "0:101 1:101", "A:1966677410;C:1379731640;G:1488012081;T:2165132052;N:78905", 101, 101, null, null, 1966677410, 1379731640, 1488012081, 2165132052, 78905, "SRX14979865", "SRS12729755", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.92364, 0.83987, 0.12298, 0.10958, 0.7289, 0.75205, 0.55329, 0.53686, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69553, "SRR18901597", "SRX14979864", "SRS12729754", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgDGAT1a 2 bulk RNAseq", "GSM6062269", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "sgDGAT1a 2 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "GSM6062269", "GSM6062269: sgDGAT1a 2 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062269 r1", "GSM6062269", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "DGAT1a_2_R1.fastq.gz DGAT1a_2_R2.fastq.gz", "fastq fastq", 8251144500.0, 40847250.0, "GSM6062269 r1", "0:101 1:101", "A:2347333328;C:1614724681;G:1750159235;T:2538833381;N:93875", 101, 101, null, null, 2347333328, 1614724681, 1750159235, 2538833381, 93875, "SRX14979864", "SRS12729754", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.91689, 0.85062, 0.17154, 0.15832, 0.7135, 0.73357, 0.55242, 0.53573, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69554, "SRR18901598", "SRX14979863", "SRS12729783", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgDGAT1a 1 bulk RNAseq", "GSM6062268", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "sgDGAT1a 1 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:DGAT1a knockout", "GSM6062268", "GSM6062268: sgDGAT1a 1 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062268 r1", "GSM6062268", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "DGAT1a_1_R1.fastq.gz DGAT1a_1_R2.fastq.gz", "fastq fastq", 18660768484.0, 92380042.0, "GSM6062268 r1", "0:101 1:101", "A:5305116678;C:3630125100;G:3862694653;T:5862619976;N:212077", 101, 101, null, null, 5305116678, 3630125100, 3862694653, 5862619976, 212077, "SRX14979863", "SRS12729783", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.91727, 0.83321, 0.16534, 0.14775, 0.71037, 0.73594, 0.53932, 0.52443, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69555, "SRR18901599", "SRX14979862", "SRS12729753", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgNT 3 bulk RNAseq", "GSM6062267", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT", "sgNT 3 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:WT", "GSM6062267", "GSM6062267: sgNT 3 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062267 r1", "GSM6062267", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "NT_3_R1.fastq.gz NT_3_R2.fastq.gz", "fastq fastq", 11541383120.0, 57135560.0, "GSM6062267 r1", "0:101 1:101", "A:3251133156;C:2311327780;G:2454133526;T:3524658644;N:130014", 101, 101, null, null, 3251133156, 2311327780, 2454133526, 3524658644, 130014, "SRX14979862", "SRS12729753", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.91632, 0.84851, 0.15351, 0.14147, 0.71366, 0.73294, 0.51256, 0.49995, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69556, "SRR18901600", "SRX14979861", "SRS12729752", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgNT 2 bulk RNAseq", "GSM6062266", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT", "sgNT 2 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:WT", "GSM6062266", "GSM6062266: sgNT 2 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062266 r1", "GSM6062266", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "NT_2_R1.fastq.gz NT_2_R2.fastq.gz", "fastq fastq", 12944530468.0, 64081834.0, "GSM6062266 r1", "0:101 1:101", "A:3642085778;C:2657512300;G:2804491849;T:3840293107;N:147434", 101, 101, null, null, 3642085778, 2657512300, 2804491849, 3840293107, 147434, "SRX14979861", "SRS12729752", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.91453, 0.86557, 0.10035, 0.0905, 0.73261, 0.7428, 0.52684, 0.51769, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69557, "SRR18901601", "SRX14979860", "SRS12729751", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "sgNT 1 bulk RNAseq", "GSM6062265", null, "source name:Skin|tissue:Skin|cell type:melanoma|genotype:WT", "sgNT 1 bulk RNAseq", "Sequencing reads underwent quality control with FASTQC 0.11.9  trimming with TRIMMOMATIC 14.0.1 and aligned using Salmon 1.4.0 to the danio rerio GRCz11. Data analysis was conducted in R version 4.0.5. Differential expression and normalized counts were calculated using DESeq2 1.30.1 using default parameters. Normalized counts derived from DESeq2 processing. Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "tissue:Skin|cell type:melanoma|genotype:WT", "GSM6062265", "GSM6062265: sgNT 1 bulk RNAseq; Danio rerio; RNA Seq", "GSM6062265 r1", "GSM6062265", "1", "Zebrafish tumors were dissected and sorted for tdTomato+ cells using the BD FACSAria cell sorter. Library construction followed the SMARTer Universal Low Input RNA Kit for Sequencing Takara according to manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "NT_1_R1.fastq.gz NT_1_R2.fastq.gz", "fastq fastq", 4065801864.0, 20127732.0, "GSM6062265 r1", "0:101 1:101", "A:1126164942;C:831186106;G:895618283;T:1212785857;N:46676", 101, 101, null, null, 1126164942, 831186106, 895618283, 1212785857, 46676, "SRX14979860", "SRS12729751", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.92125, 0.86236, 0.09794, 0.08896, 0.73148, 0.7457, 0.52439, 0.51074, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "full_length", "cdna_unspecified", "smarter", "sc_generic", "bulk", "bulk", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69558, "SRR18901602", "SRX14979859", "SRS12729750", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "TEAZ scRNAseq", "GSM6062264", null, "source name:Skin|tissue:Skin|cell type:melanoma", "TEAZ scRNAseq", "Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 and Chromium Single Cell 3\u2019 Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:\u00a0 Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "tissue:Skin|cell type:melanoma", "GSM6062264", "GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq", "GSM6062264 r1", "GSM6062264", "1", "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "2544_PTEN_combined_IGO_11963_4_S2_L001_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L001_R2_001.fastq.gz", "fastq fastq", 9314576760.0, 77621473.0, "GSM6062264 r1", "0:29 1:91", "A:2571624849;C:2103171866;G:2248508025;T:2390911966;N:360054", 29, 91, null, null, 2571624849, 2103171866, 2248508025, 2390911966, 360054, "SRX14979859", "SRS12729750", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00434, 0.8777, 0.00177, 0.14429, 0.99253, 0.78492, 0.35282, 0.53036, 29, 91, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69559, "SRR18901603", "SRX14979859", "SRS12729750", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "TEAZ scRNAseq", "GSM6062264", null, "source name:Skin|tissue:Skin|cell type:melanoma", "TEAZ scRNAseq", "Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 and Chromium Single Cell 3\u2019 Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:\u00a0 Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "tissue:Skin|cell type:melanoma", "GSM6062264", "GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq", "GSM6062264 r1", "GSM6062264", "1", "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "2544_PTEN_combined_IGO_11963_4_S2_L002_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L002_R2_001.fastq.gz", "fastq fastq", 9122357880.0, 76019649.0, "GSM6062264 r2", "0:29 1:91", "A:2521047948;C:2056950129;G:2200048731;T:2343919901;N:391171", 29, 91, null, null, 2521047948, 2056950129, 2200048731, 2343919901, 391171, "SRX14979859", "SRS12729750", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00471, 0.87992, 0.00196, 0.14374, 0.99255, 0.78476, 0.35593, 0.54484, 29, 91, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69560, "SRR18901604", "SRX14979859", "SRS12729750", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "TEAZ scRNAseq", "GSM6062264", null, "source name:Skin|tissue:Skin|cell type:melanoma", "TEAZ scRNAseq", "Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 and Chromium Single Cell 3\u2019 Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:\u00a0 Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "tissue:Skin|cell type:melanoma", "GSM6062264", "GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq", "GSM6062264 r1", "GSM6062264", "1", "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "2544_PTEN_combined_IGO_11963_4_S2_L003_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L003_R2_001.fastq.gz", "fastq fastq", 9307586160.0, 77563218.0, "GSM6062264 r3", "0:29 1:91", "A:2569072609;C:2102732051;G:2247036264;T:2388393636;N:351600", 29, 91, null, null, 2569072609, 2102732051, 2247036264, 2388393636, 351600, "SRX14979859", "SRS12729750", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00429, 0.87889, 0.00178, 0.1429, 0.99271, 0.78589, 0.35728, 0.54587, 29, 91, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"], [69561, "SRR18901605", "SRX14979859", "SRS12729750", "SRP371883", "PRJNA831276", "Lipid droplets are a metabolic vulnerability in melanoma", "GSE201378", "Transcriptome Analysis", "Melanoma exhibits numerous transcriptional cell states including neural crest like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here  we use a zebrafish melanoma model to identify a transcriptional program linking the melanocytic cell state to a dependence on lipid droplets  the specialized organelle responsible for lipid storage. Single cell RNA sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved across human melanoma cell lines and patient tumors. This melanocytic state demonstrates increased fatty acid uptake  an increased number of lipid droplets  and dependence upon fatty acid oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt cell cycle progression and slow melanoma growth in vivo. Because the melanocytic cell state is linked to poor outcomes in patients  these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle. Overall design: Expression profiling by high throughput sequencing of zebrafish melanoma", null, "pubmed:37268606", null, "TEAZ scRNAseq", "GSM6062264", null, "source name:Skin|tissue:Skin|cell type:melanoma", "TEAZ scRNAseq", "Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Counts matrix derived from Seurat Data was processed using R version 4.0.5 and Seurat version 4.0.2. Cells with fewer than 200 unique genes and mitochondrial genes above 30% were filtered. Expression data was normalized using SCTransform with principal component analysis and UMAP dimensionality reduction performed at default parameters. Clustering was performed using the Seurat function FindClusters with resolution of 0.4. Cluster annotation for zebrafish cell type specific marker genes as done previously using FindAllMarkers. Assembly: GRCz11", "Skin", null, "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell 3\u2019 Library and Gel Bead Kit v3 and Chromium Single Cell 3\u2019 Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:\u00a0 Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "tissue:Skin|cell type:melanoma", "GSM6062264", "GSM6062264: TEAZ scRNAseq; Danio rerio; RNA Seq", "GSM6062264 r1", "GSM6062264", "1", "Zebrafish tumors were dissected and dissociated for encapsulation Library preparation and sequencing were done by the Single Cell Research Initiative and Integrated Genomics Organization at MSKCC. For cell encapsulation and library preparation  droplet based scRNA seq was performed on approximately 5900 cells using the Chromium Single Cell three prime Library and Gel Bead Kit v3 and Chromium Single Cell three prime Chip G 10x Genomics into a single v3 reaction. GEM generation and library preparation were performed according to manufacturer instructions. Libraries were sequenced on a NovaSeq6000. Sequencing parameters:  Read1 28 cycles  i5 10 cycles  i7 10 cycles  Read2 90 cycles. Sequencing depth was approximately 51 000 reads per cell. Sequencing data was aligned to our reference zebrafish genome using CellRanger 6.0.2.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP371883", null, "loader:fastq load.py", "2544_PTEN_combined_IGO_11963_4_S2_L004_R1_001.fastq.gz 2544_PTEN_combined_IGO_11963_4_S2_L004_R2_001.fastq.gz", "fastq fastq", 9382270920.0, 78185591.0, "GSM6062264 r4", "0:29 1:91", "A:2591803792;C:2116313097;G:2264892157;T:2408930364;N:331510", 29, 91, null, null, 2591803792, 2116313097, 2264892157, 2408930364, 331510, "SRX14979859", "SRS12729750", "SRA1408865", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", "Richard M. White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center", 2, 0.00445, 0.87912, 0.00184, 0.14625, 0.99287, 0.78573, 0.37029, 0.5207, 29, 91, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-04-23", "Undetermined", "Undetermined", "Skin", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 19, "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_coarse\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "Skin"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, 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"results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&tissue_curation=Skin&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&tissue_curation=Skin", "results": [{"value": "Skin", "label": "Skin", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&tissue_curation=Skin", "results": [{"value": "bulk", "label": "bulk", "count": 12, "toggle_url": 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