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 61390,SRR12708451,SRX9187386,SRS7423761,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFN3,GSM4802478,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFN3,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802478,GSM4802478: MFN3; Danio rerio; RNA Seq,GSM4802478,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802478,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFN3_R1_001.fastq.gz MFN3_R2_001.fastq.gz,fastq fastq,14558703600.0,48529012.0,GSM4802478 r1,0:150 1:150,A:3871514784;C:3434394240;G:3331911824;T:3919968300;N:914452,150,150,,,3871514784,3434394240,3331911824,3919968300,914452,SRX9187386,SRS7423761,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89707,0.89196,0.05724,0.05696,0.75396,0.75597,0.43181,0.41631,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61391,SRR12708450,SRX9187385,SRS7423760,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFG3,GSM4802477,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFG3,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802477,GSM4802477: MFG3; Danio rerio; RNA Seq,GSM4802477,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802477,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFG3_R1_001.fastq.gz MFG3_R2_001.fastq.gz,fastq fastq,10045323900.0,33484413.0,GSM4802477 r1,0:150 1:150,A:2619233046;C:2425417526;G:2312268655;T:2687771920;N:632753,150,150,,,2619233046,2425417526,2312268655,2687771920,632753,SRX9187385,SRS7423760,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90365,0.90046,0.06439,0.06489,0.75436,0.75641,0.54634,0.54693,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61394,SRR12708447,SRX9187382,SRS7423757,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFN3,GSM4802474,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFN3,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802474,GSM4802474: XFN3; Danio rerio; RNA Seq,GSM4802474,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802474,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFN3_R1_001.fastq.gz XFN3_R2_001.fastq.gz,fastq fastq,11204873700.0,37349579.0,GSM4802474 r1,0:150 1:150,A:2943394483;C:2667470839;G:2579644073;T:3013655182;N:709123,150,150,,,2943394483,2667470839,2579644073,3013655182,709123,SRX9187382,SRS7423757,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90055,0.89407,0.05457,0.05489,0.74247,0.746,0.48492,0.48602,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61395,SRR12708446,SRX9187381,SRS7423756,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFG3,GSM4802473,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFG3,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802473,GSM4802473: XFG3; Danio rerio; RNA Seq,GSM4802473,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802473,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFG3_R1_001.fastq.gz XFG3_R2_001.fastq.gz,fastq fastq,11212083000.0,37373610.0,GSM4802473 r1,0:150 1:150,A:2979985262;C:2652925544;G:2513147966;T:3065318302;N:705926,150,150,,,2979985262,2652925544,2513147966,3065318302,705926,SRX9187381,SRS7423756,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.9056,0.89972,0.06159,0.06165,0.74194,0.74602,0.49523,0.44889,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61398,SRR12708443,SRX9187378,SRS7423753,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFN2,GSM4802470,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFN2,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802470,GSM4802470: MFN2; Danio rerio; RNA Seq,GSM4802470,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802470,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFN2_R1_001.fastq.gz MFN2_R2_001.fastq.gz,fastq fastq,9002969100.0,30009897.0,GSM4802470 r1,0:150 1:150,A:2383579322;C:2152753900;G:2013843514;T:2452228154;N:564210,150,150,,,2383579322,2152753900,2013843514,2452228154,564210,SRX9187378,SRS7423753,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89613,0.89129,0.06896,0.06936,0.75235,0.75659,0.51059,0.50763,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61399,SRR12708442,SRX9187377,SRS7423752,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFG2,GSM4802469,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFG2,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802469,GSM4802469: MFG2; Danio rerio; RNA Seq,GSM4802469,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802469,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFG2_R1_001.fastq.gz MFG2_R2_001.fastq.gz,fastq fastq,11893039800.0,39643466.0,GSM4802469 r1,0:150 1:150,A:3160384920;C:2834257771;G:2698430613;T:3199226169;N:740327,150,150,,,3160384920,2834257771,2698430613,3199226169,740327,SRX9187377,SRS7423752,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90353,0.89813,0.06957,0.06993,0.75183,0.75607,0.46098,0.51543,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61402,SRR12708439,SRX9187374,SRS7423749,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFN2,GSM4802466,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFN2,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802466,GSM4802466: XFN2; Danio rerio; RNA Seq,GSM4802466,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802466,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFN2_R1_001.fastq.gz XFN2_R2_001.fastq.gz,fastq fastq,11313005400.0,37710018.0,GSM4802466 r1,0:150 1:150,A:2996096346;C:2703585714;G:2550898118;T:3061720444;N:704778,150,150,,,2996096346,2703585714,2550898118,3061720444,704778,SRX9187374,SRS7423749,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.88653,0.88127,0.06171,0.06088,0.74856,0.75252,0.51699,0.51503,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61403,SRR12708438,SRX9187373,SRS7423748,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFG2,GSM4802465,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFG2,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802465,GSM4802465: XFG2; Danio rerio; RNA Seq,GSM4802465,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802465,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFG2_R1_001.fastq.gz XFG2_R2_001.fastq.gz,fastq fastq,11921269800.0,39737566.0,GSM4802465 r1,0:150 1:150,A:3191695537;C:2823855056;G:2636104989;T:3268877243;N:736975,150,150,,,3191695537,2823855056,2636104989,3268877243,736975,SRX9187373,SRS7423748,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89811,0.89304,0.06734,0.0674,0.7391,0.74261,0.51932,0.45328,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61406,SRR12708435,SRX9187370,SRS7423745,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFN1,GSM4802462,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFN1,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802462,GSM4802462: MFN1; Danio rerio; RNA Seq,GSM4802462,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802462,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFN1_R1_001.fastq.gz MFN1_R2_001.fastq.gz,fastq fastq,12560283900.0,41867613.0,GSM4802462 r1,0:150 1:150,A:3295279231;C:3013386640;G:2898979550;T:3351847365;N:791114,150,150,,,3295279231,3013386640,2898979550,3351847365,791114,SRX9187370,SRS7423745,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.89681,0.89104,0.06566,0.06589,0.74272,0.74791,0.51645,0.51902,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61407,SRR12708434,SRX9187369,SRS7423744,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,MFG1,GSM4802461,,tissue:Zebrafish fins|strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin,MFG1,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Wildtype melanocyte model Caspers with MiniCoopR eGFP|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802461,GSM4802461: MFG1; Danio rerio; RNA Seq,GSM4802461,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802461,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,MFG1_R1_001.fastq.gz MFG1_R2_001.fastq.gz,fastq fastq,11317873500.0,37726245.0,GSM4802461 r1,0:150 1:150,A:2947830189;C:2733463243;G:2616872694;T:3018996791;N:710583,150,150,,,2947830189,2733463243,2616872694,3018996791,710583,SRX9187369,SRS7423744,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90788,0.90139,0.06383,0.06478,0.74268,0.74686,0.50725,0.50595,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61410,SRR12708431,SRX9187366,SRS7423741,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFN1,GSM4802458,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFN1,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP ,GSM4802458,GSM4802458: XFN1; Danio rerio; RNA Seq,GSM4802458,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802458,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFN1_R1_001.fastq.gz XFN1_R2_001.fastq.gz,fastq fastq,11573931900.0,38579773.0,GSM4802458 r1,0:150 1:150,A:2999184334;C:2801583964;G:2672180906;T:3100254047;N:728649,150,150,,,2999184334,2801583964,2672180906,3100254047,728649,SRX9187366,SRS7423741,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.8962,0.88921,0.05791,0.05848,0.74097,0.7471,0.50594,0.5107,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure 61411,SRR12708430,SRX9187365,SRS7423740,SRP285315,PRJNA665531,Bulk RNA seq of fin and body melanocytes and microenvironments,GSE158538,Transcriptome Analysis,Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: 1 cell lineage: melanocyte vs bulk microenvironment 2 anatomic location: fin vs body 3 genotype: wildtype vs CRKL GAB2 TERT overexpression with NF1 loss. We found that melanocytes have unique transcriptional programs based on their anatomic location and that these programs can regulate the response to oncogenic drivers like CRKL. Overall design: For this experiment we used two genetic strains of zebrafish. 1 Wildtype melanocyte model stable line was generated by injecting Caspers with MiniCoopR eGFP. 2 Acral melanoma model stable line was generated by injecting Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA. Fish were dissected to collect body skin and fins digested using liberase and then FACS sorted for GFP+ melanocytes and GFP microenvironment cells. Each biological replicate constituted a pooling of 2 males and 2 females. There were 2 genetic strainsWT v Acral x 2 anatomic locationsfin v body x 2 sorted conditionsGFP+ v GFP x 3 biological replicates = 24 samples total.,,pubmed:35355015,,XFG1,GSM4802457,,tissue:Zebrafish fins|strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry; U6 nf1a gRNA mitfa:Cas9 mCherry; U6 nf1b gRNA|anatomic location:Fin,XFG1,md5sum to confirm files copied to server without xxx; FastQC for all files; Trimmomatic for all files to remove adaptor sequences and low quality sequences; FastQC for all files; STAR to align to GRCz10 Ensemble version 81 and get both BAM file and counts table as output; SeQC on aligned BAM file for each sample. Genome build: GRCz10 Supplementary files format and content: tab delimited text file for every sample with raw counts for every gene Supplementary files format and content: table with raw counts for every gene and every sample with genes annotated,Zebrafish fins,,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,,strain:Acral melanoma model Caspers with MiniCoopR eGFP mitfa:hsCRKL mitfa:hsGAB2 mitfa:hsTERT mitfa:Cas9 mCherry;U6 nf1a gRNA mitfa:Cas9 mCherry;U6 nf1b gRNA|anatomic location:Fin|gfp+ or gfp :GFP+,GSM4802457,GSM4802457: XFG1; Danio rerio; RNA Seq,GSM4802457,,1,Cells were FACS sorted into TRIZOL LS and snap frozen. Total RNA was extracted using TRIZOL LS protocol. Total RNA varied from 1.2ng to 150ng all having RIN scores > 7. Reverse transcription and cDNA amplification were performed with SMART Seq v4 Ultra Low Input RNA Kit Clontech. Libraries were constructed using Illumina Nextera XT kit and analyzed for concentration Qubit size distribribution Agilent Bioanalyzer.,GEO Accession:GSM4802457,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP285315,,,XFG1_R1_001.fastq.gz XFG1_R2_001.fastq.gz,fastq fastq,11738198700.0,39127329.0,GSM4802457 r1,0:150 1:150,A:3083667179;C:2816699592;G:2648683281;T:3188411465;N:737183,150,150,,,3083667179,2816699592,2648683281,3188411465,737183,SRX9187365,SRS7423740,SRA1131319,GEO,"White, Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center",2,0.90455,0.89777,0.05668,0.05707,0.74631,0.75057,0.49373,0.48957,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,nextera,sc,single_cell_plate,smartseq,,United States,2020-09-24,Undetermined,Undetermined,Fin,Surface Structure