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 32858,SRR29482326,SRX24993370,SRS21694834,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Internal melanocytes,GSM8340241,,source name:Internal melanocytes|tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Internal melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Internal melanocytes,,Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Internal melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP,GSM8340241,GSM8340241: Internal melanocytes; Danio rerio; OTHER,GSM8340241 r1,GSM8340241,1,Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-002_H5GCWBGXF_R2.fastq.gz HAR-MI-002_H5GCWBGXF_R1.fastq.gz,fastq fastq,2957975418.0,34395063.0,GSM8340241 r1,0:26 1:60,A:738954503;C:560052455;G:520746060;T:1137116132;N:1106268,26,60,,,738954503,560052455,520746060,1137116132,1106268,SRX24993370,SRS21694834,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11637,0.84116,0.10894,0.31188,0.98851,0.71526,0.6688,0.60221,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure 32859,SRR29482327,SRX24993369,SRS21694833,SRP515140,PRJNA1126247,Specific oncogene activation of the cell of origin in mucosal melanoma [SORT seq],GSE270356,Other,Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Single cell RNA sequencing was done on internal vs. external normal adult zebrafish melanocytes using the SORT seq platform.,,,,Cutaneous melanocytes,GSM8340240,,source name:Cutaneous melanocytes|tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP|geo loc name:missing|collection date:missing,Cutaneous melanocytes,BWA was used to align paired end read to danRer11. Count tables were generated using MapAndGo. Count tables were corrected using UMI to remove duplicate reads. Transcript counts were adjusted using Poissonian counting statistics to yield the number of UMIs detected per cell. Counts were imported into R using the Seurat suite version 3.0 Assembly: danRer11 Supplementary files format and content: .tsv file contains count matrix file used for data normalization and visualization using Seurat Library strategy: SORT seq,Cutaneous melanocytes,,Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,mitfa / ; roy / zebrafish injected with mitfa:GFP were Raised to maturity to obtain tissues,tissue:Cutaneous melanocytes|cell type:melanocytes|genotype:mitfa / ; roy / fish injected with mitfa:GFP,GSM8340240,GSM8340240: Cutaneous melanocytes; Danio rerio; OTHER,GSM8340240 r1,GSM8340240,1,Respective tissues were mechanically dissociated digested in TrypLE for 45 min Invitrogen 12563011 40uM filtered spun down and resuspended in FACs buffer dPBS Mg+/Ca+ free with 2% FBS pen/strep. Cells were heat lysed at 65°C followed by cDNA synthesis with barcodes. All the barcoded material from one plate was pooled into one library and amplified using in vitro transcription. Following amplification library preparation was done following the CEL Seq2 protocol to prepare a cDNA library for sequencing using TruSeq small RNA primers Illumina.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP515140,,,HAR-MI-001_H5GCWBGXF_R2.fastq.gz HAR-MI-001_H5GCWBGXF_R1.fastq.gz,fastq fastq,2680460212.0,31168142.0,GSM8340240 r1,0:26 1:60,A:704357434;C:519158361;G:467098420;T:988838604;N:1007393,26,60,,,704357434,519158361,467098420,988838604,1007393,SRX24993369,SRS21694833,SRA1904773,"Insco Lab, Medical Oncology, Dana Farber Cancer Institute","Insco Lab, Medical Oncology, Dana Farber Cancer Institute",2,0.11679,0.81545,0.10693,0.5033,0.9808,0.76404,0.44749,0.57623,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,small_rna,trueseq,sc,single_cell_plate,celseq,,United States,2024-06-20,Undetermined,Adult,Skin,Surface Structure 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.,,,,m4b mut melanoma biol rep 2,GSM8552314,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,785806700,949078797,1178279032,784972987,7227109,SRX26263941,SRS22803195,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,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.,,,,m4b mut melanoma biol rep 1,GSM8552313,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,1016908920,1236613888,1502465334,1018053808,5335422,SRX26263940,SRS22803194,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,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.,,,,wild type melanoma control biol rep 2,GSM8552312,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,1136639418,1414638483,1736492639,1137614638,1994331,SRX26263939,SRS22803193,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,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.,,,,wild type melanoma control biol rep 1,GSM8552311,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,1112163842,1354895660,1658732932,1120342985,1973538,SRX26263938,SRS22803192,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,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.,,,,melanophore biol rep 2,GSM8552310,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,1114533149,1104066636,1293649625,1122672029,1710442,SRX26263937,SRS22803191,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,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.,,,,melanophore biol rep 1,GSM8552309,,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,,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,,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,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 2000,,SRP536275,,,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,,,1231235669,1235759770,1476864583,1240636871,1264353,SRX26263936,SRS22803190,SRA1984938,"Pigment Cell Biology Lab, CSIR-IGIB","Pigment Cell Biology Lab, CSIR-IGIB",,,,,,,,,,,,B,B,biological fallback assumption,illumina,nextseq_v2,unknown,cdna_unspecified,trueseq,sc_generic,bulk,bulk,,India,2024-10-02,Undetermined,Undetermined,Skin,Surface Structure 52154,SRR18181452,SRX14328416,SRS12144047,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin6,GSM5924290,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin6,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924290,GSM5924290: Skin6; Danio rerio; RNA Seq,GSM5924290,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924290,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin6.bam,bam,25513490100.0,85044967.0,GSM5924290 r1,0:150 1:150,A:6925113942;C:3968740165;G:4171395948;T:10445470654;N:2769391,150,150,,,6925113942,3968740165,4171395948,10445470654,2769391,SRX14328416,SRS12144047,SRA880843,GEO,Zhejiang University,2,2e-05,0.59157,0.0,0.06443,0.99997,0.87677,1.0,0.63522,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 52155,SRR18181451,SRX14328415,SRS12144046,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin5,GSM5924289,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin5,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924289,GSM5924289: Skin5; Danio rerio; RNA Seq,GSM5924289,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924289,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin5.bam,bam,28489208700.0,94964029.0,GSM5924289 r1,0:150 1:150,A:8246685822;C:4290659458;G:4422543987;T:11526089448;N:3229985,150,150,,,8246685822,4290659458,4422543987,11526089448,3229985,SRX14328415,SRS12144046,SRA880843,GEO,Zhejiang University,2,0.0,0.52,0.0,0.05199,1.0,0.89509,,0.61209,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 52156,SRR18181450,SRX14328414,SRS12144045,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin3,GSM5924288,,source name:skin|strain:Tubingen|tissue:skin|genotype:wild type,Skin3,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:skin|genotype:wild type,GSM5924288,GSM5924288: Skin3; Danio rerio; RNA Seq,GSM5924288,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924288,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Skin3.bam,bam,22656818700.0,75522729.0,GSM5924288 r1,0:150 1:150,A:5656101080;C:3775541088;G:3901788913;T:9321421770;N:1965849,150,150,,,5656101080,3775541088,3901788913,9321421770,1965849,SRX14328414,SRS12144045,SRA880843,GEO,Zhejiang University,2,2e-05,0.77804,0.0,0.0376,0.99997,0.77275,1.0,0.58426,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Skin,Surface Structure 52201,SRR8991405,SRX5770473,SRS4704582,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022.,,pubmed:34660600,,Skin4,GSM3740958,,source name:skin|strain:Tubingen|genotype:wild type|tissue:skin,Skin4,The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes.,skin,,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:skin,GSM3740958,GSM3740958: Skin4; Danio rerio; RNA Seq,GSM3740958,,1,Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740958,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Skin4.bam,bam,33628232728.0,111351764.0,GSM3740958 r1,0:151 1:151,A:8460681247;C:5738320863;G:5953293918;T:13386336300;N:89600400,151,151,,,8460681247,5738320863,5953293918,13386336300,89600400,SRX5770473,SRS4704582,SRA880843,GEO,Zhejiang University,2,0.0,0.73034,0.0,0.03701,1.0,0.80454,,0.53563,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,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.,,pubmed:34556579,,Skin3,GSM5237137,,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,,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°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:skin|strain:TLAB,GSM5237137,GSM5237137: Skin3; Danio rerio; RNA Seq,GSM5237137,,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,,SRP314470,,,Skin3.fastq,fastq,1791301700.0,17913017.0,GSM5237137 r1,0:100,A:461644132;C:423476905;G:420663755;T:485448242;N:68666,100,,,,461644132,423476905,420663755,485448242,68666,SRX10579913,SRS8684381,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95551,,0.07734,,0.76828,,0.55723,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,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.,,pubmed:34556579,,Skin2,GSM5237136,,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,,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°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:skin|strain:TLAB,GSM5237136,GSM5237136: Skin2; Danio rerio; RNA Seq,GSM5237136,,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,,SRP314470,,,Skin2.fastq,fastq,1540878000.0,15408780.0,GSM5237136 r1,0:100,A:394401295;C:368888243;G:364934471;T:412595940;N:58051,100,,,,394401295,368888243,364934471,412595940,58051,SRX10579912,SRS8684380,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.94678,,0.09904,,0.75306,,0.54337,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,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.,,pubmed:34556579,,Skin1,GSM5237135,,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,,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°C water temperature; 14/10 hour light/dark cycle,genotype:wild type|tissue:skin|strain:TLAB,GSM5237135,GSM5237135: Skin1; Danio rerio; RNA Seq,GSM5237135,,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,,SRP314470,,,Skin1.fastq,fastq,1894948100.0,18949481.0,GSM5237135 r1,0:100,A:486879091;C:450700393;G:453217896;T:504078083;N:72637,100,,,,486879091,450700393,453217896,504078083,72637,SRX10579911,SRS8684379,SRA1217576,GEO,"Pauli lab, Research Institute of Molecular Pathology",1,0.95498,,0.07021,,0.75986,,0.55816,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,nebnext,bulk,unknown,unknown,,Austria,2021-04-12,Undetermined,Undetermined,Skin,Surface Structure 65018,SRR14902688,SRX11217410,SRS9271509,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC Het3 RNAseq,GSM5397955,,source name:Sorted skin|genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes,MC Het3 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397955,GSM5397955: MC Het3 RNAseq; Danio rerio; RNA Seq,GSM5397955,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397955,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_Het3.fq.gz,fastq,1406637500.0,28132750.0,GSM5397955 r1,0:50 1:0,A:395401471;C:296267357;G:292837098;T:421133953;N:997621,50,0,,,395401471,296267357,292837098,421133953,997621,SRX11217410,SRS9271509,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.85386,,0.16676,,0.7599,,0.50494,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Skin,Surface Structure 65019,SRR14902687,SRX11217409,SRS9271508,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC Het2 RNAseq,GSM5397954,,source name:Sorted skin|genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes,MC Het2 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397954,GSM5397954: MC Het2 RNAseq; Danio rerio; RNA Seq,GSM5397954,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397954,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_Het2.fq.gz,fastq,1210667450.0,24213349.0,GSM5397954 r1,0:50 1:0,A:339770058;C:251491491;G:247052776;T:371493471;N:859654,50,0,,,339770058,251491491,247052776,371493471,859654,SRX11217409,SRS9271508,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.82621,,0.1611,,0.76479,,0.50839,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Skin,Surface Structure 65020,SRR14902686,SRX11217408,SRS9271507,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC Het1 RNAseq,GSM5397953,,source name:Sorted skin|genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes,MC Het1 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:BRAFV600E/+/p53+/lf/mitfa+/ /mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397953,GSM5397953: MC Het1 RNAseq; Danio rerio; RNA Seq,GSM5397953,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397953,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_Het1.fq.gz,fastq,1384374750.0,27687495.0,GSM5397953 r1,0:50 1:0,A:388802638;C:286808201;G:284844887;T:422934445;N:984579,50,0,,,388802638,286808201,284844887,422934445,984579,SRX11217408,SRS9271507,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.83734,,0.17265,,0.75339,,0.53771,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Skin,Surface Structure 65021,SRR14902685,SRX11217407,SRS9271506,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC WT3 RNAseq,GSM5397952,,source name:Sorted skin|genotype:mitfa:mCherry|tissue:Skin melanocytes,MC WT3 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397952,GSM5397952: MC WT3 RNAseq; Danio rerio; RNA Seq,GSM5397952,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397952,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_WT3.fq.gz,fastq,1608392500.0,32167850.0,GSM5397952 r1,0:50 1:0,A:450203217;C:338134607;G:334610507;T:484299941;N:1144228,50,0,,,450203217,338134607,334610507,484299941,1144228,SRX11217407,SRS9271506,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.84877,,0.14531,,0.76822,,0.52491,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Skin,Surface Structure 65022,SRR14902684,SRX11217406,SRS9271505,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC WT2 RNAseq,GSM5397951,,source name:Sorted skin|genotype:mitfa:mCherry|tissue:Skin melanocytes,MC WT2 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397951,GSM5397951: MC WT2 RNAseq; Danio rerio; RNA Seq,GSM5397951,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397951,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_WT2.fq.gz,fastq,1487158350.0,29743167.0,GSM5397951 r1,0:50 1:0,A:415644842;C:312248816;G:308870370;T:449336856;N:1057466,50,0,,,415644842,312248816,308870370,449336856,1057466,SRX11217406,SRS9271505,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.83832,,0.16784,,0.75294,,0.4934,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,Skin,Surface Structure 65023,SRR14902683,SRX11217405,SRS9271504,SRP325444,PRJNA741108,Transcriptional Profile in Zebrafish Melanocytes and Melanoma Tumors [RNA seq],GSE178801,Transcriptome Analysis,With high genetic heterogeneity in melanoma understanding epigenetic and transcriptional differences between melanocytes and melanoma cells will enable further understanding of the genes pathways and epigenetic regions influencing melanoma development. We performed RNA seq and ATAC seq on fluorescently isolated melanocytes and melanoma cells from a zebrafish melanoma model. Overall design: RNA seq profiles of FACS isolated mitfa:mCherry reporter positive melanocytes and crestin:GFP positive melanoma cells from adult zebrafish D. rerio.,parent bioproject:PRJNA741103,pubmed:34791221,,MC WT1 RNAseq,GSM5397950,,source name:Sorted skin|genotype:mitfa:mCherry|tissue:Skin melanocytes,MC WT1 RNAseq,Assess read quality with FastQC Align to GRCz11/danRer11 using STAR Quantify transcriptome using RSEM Normalize reads with DESeq2 Genome build: danRer11 Supplementary files format and content: tab delimited text files with CPM values for each sample Supplementary files format and content: tab delimited text files with RPKM values for each sample Supplementary files format and content: Excel spreadsheet summarizing log2FC values between melanocytes and melanoma cells as well as,Sorted skin,,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,,genotype:mitfa:mCherry|tissue:Skin melanocytes|run #:1,GSM5397950,GSM5397950: MC WT1 RNAseq; Danio rerio; RNA Seq,GSM5397950,,1,FACS for fluorescent tag: mCherry for melanocytes MC and GFP for melanoma cells MA then use Machery Nagel kit to extract total RNA cDNA generated using Clontech SMARTer cDNA amplification kit,GEO Accession:GSM5397950,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP325444,,,MC_WT1.fq.gz,fastq,1492507300.0,29850146.0,GSM5397950 r1,0:50 1:0,A:414126211;C:315863559;G:313307227;T:448149699;N:1060604,50,0,,,414126211,315863559,313307227,448149699,1060604,SRX11217405,SRS9271504,SRA1250059,GEO,"Kaufman, Oncology, Washington University in St. Louis",1,0.84681,,0.13522,,0.77419,,0.44296,,50,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United States,2021-06-24,Undetermined,Adult,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,,pubmed:37268606,,sgDGAT1a 3 bulk RNAseq,GSM6062270,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,sgDGAT1a 2 bulk RNAseq,GSM6062269,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,sgDGAT1a 1 bulk RNAseq,GSM6062268,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,sgNT 3 bulk RNAseq,GSM6062267,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,sgNT 2 bulk RNAseq,GSM6062266,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,sgNT 1 bulk RNAseq,GSM6062265,,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,,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.,,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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,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,,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’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ 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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,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,,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’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ 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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,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,,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’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ 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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,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,,pubmed:37268606,,TEAZ scRNAseq,GSM6062264,,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,,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’ Library and Gel Bead Kit v3 and Chromium Single Cell 3’ 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.,,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.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP371883,,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,,,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,,United States,2022-04-23,Undetermined,Undetermined,Skin,Surface Structure