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
50529,SRR8129708,SRX4950830,SRS3993021,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2 replicate b,GSM3449969,,tissue:Fli:GFP  sorted  3 days  RNeasy sample 2  replicate b|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2 replicate b,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNeasy sample 2  replicate b,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449969,GSM3449969: RNeasy sorted 2 replicate b; Danio rerio; RNA Seq,GSM3449969,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449969,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,Q_2b_R1.fastq.gz Q_2b_R2.fastq.gz,fastq fastq,3579768697.0,23697156.0,GSM3449969 r1,0:75.53 1:75.53,A:917613628;C:877326634;G:877017498;T:907801181;N:9756,75,75,,,917613628,877326634,877017498,907801181,9756,SRX4950830,SRS3993021,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93264,0.93171,0.08657,0.08851,0.73878,0.74383,0.48764,0.4769,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50530,SRR8129707,SRX4950829,SRS3993019,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2 replicate a,GSM3449968,,tissue:Fli:GFP  sorted  3 days  RNeasy sample 2  replicate a|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2 replicate a,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNeasy sample 2  replicate a,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449968,GSM3449968: RNeasy sorted 2 replicate a; Danio rerio; RNA Seq,GSM3449968,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449968,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,Q_2a_R1.fastq.gz Q_2a_R2.fastq.gz,fastq fastq,3145186655.0,20819322.0,GSM3449968 r1,0:75.54 1:75.54,A:794507127;C:779916130;G:782068102;T:788686496;N:8800,75,75,,,794507127,779916130,782068102,788686496,8800,SRX4950829,SRS3993019,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93181,0.93429,0.07677,0.08034,0.73703,0.74736,0.49133,0.47929,76,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50531,SRR8129706,SRX4950828,SRS3993020,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 2 replicate b,GSM3449967,,tissue:Fli:GFP  sorted  3 days  RNAqueous  sample 2  replicate b|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 2 replicate b,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNAqueous  sample 2  replicate b,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449967,GSM3449967: RNAqueous sorted 2 replicate b; Danio rerio; RNA Seq,GSM3449967,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449967,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,A_2b_R2.fastq.gz A_2b_R1.fastq.gz,fastq fastq,2391676247.0,15831796.0,GSM3449967 r1,0:75.53 1:75.53,A:602794312;C:593325110;G:594803186;T:600747475;N:6164,75,75,,,602794312,593325110,594803186,600747475,6164,SRX4950828,SRS3993020,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.9382,0.93646,0.08421,0.08835,0.73919,0.7502,0.48177,0.485,76,76,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50532,SRR8129705,SRX4950827,SRS3993018,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 2 replicate a,GSM3449966,,tissue:Fli:GFP  sorted  3 days  RNAqueous  sample 2  replicate a|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 2 replicate a,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNAqueous  sample 2  replicate a,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449966,GSM3449966: RNAqueous sorted 2 replicate a; Danio rerio; RNA Seq,GSM3449966,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449966,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP167139,,,A_2a_R1.fastq.gz A_2a_R2.fastq.gz,fastq fastq,3489621694.0,23100721.0,GSM3449966 r1,0:75.53 1:75.53,A:884597345;C:865637159;G:859062299;T:880315566;N:9325,75,75,,,884597345,865637159,859062299,880315566,9325,SRX4950827,SRS3993018,SRA800291,GEO,"Center for Medical Genetics, Ghent University",2,0.93703,0.93839,0.09176,0.09203,0.73381,0.73206,0.46533,0.47636,75,75,B,B,biological fallback assumption,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50533,SRR8129704,SRX4950826,SRS3993016,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNeasy sorted 2,GSM3449965,,tissue:Fli:GFP  sorted  3 days  RNeasy sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,RNeasy sorted 2,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNeasy sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNeasy plus micro kit,GSM3449965,GSM3449965: RNeasy sorted 2; Danio rerio; RNA Seq,GSM3449965,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449965,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,Q_1.fastq.gz,fastq,1059463914.0,14029229.0,GSM3449965 r1,0:75.52 1:0,A:284634446;C:242976410;G:245781627;T:286026099;N:45332,75,0,,,284634446,242976410,245781627,286026099,45332,SRX4950826,SRS3993016,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.91903,,0.09754,,0.73537,,0.48738,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
50534,SRR8129703,SRX4950825,SRS3993017,SRP167139,PRJNA499073,Purification of high quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes,GSE121917,Transcriptome Analysis,We provide a method for high quality RNA purification out of a small number 5000   100 000 of FACS sorted zebrafish cells followed by RNA sequencing Overall design: RNA sequencing data from 6 RNA samples isolated from 20000 sorted fli:GFP zebrafish cells. 2 RNA samples isolated from whole embryo.,,pubmed:30894119,,RNAqueous sorted 1,GSM3449964,,tissue:Fli:GFP  sorted  3 days  RNAqueous  sample 1|cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,RNAqueous sorted 1,Fastq files were aligned to GRCz10 with STAR v2 4 2a. Gene quantification was done on the fly by STAR on Danio rerio.GRCz10.91.gtf Genome build: GRCz10 Supplementary files format and content: tsv files with raw count data,Fli:GFP  sorted  3 days  RNAqueous  sample 1,,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,,cell type:fli:GFP  GFP sorted|age:3 days|rna isolation kit:RNAqueous micro,GSM3449964,GSM3449964: RNAqueous sorted 1; Danio rerio; RNA Seq,GSM3449964,,1,polyA RNA cDNA was synthesized according to the SMART seq V4 takara biosystems technology  tagmentation and sample barcoding with the Nextera XT kit illumina,GEO Accession:GSM3449964,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP167139,,,A_1.fastq.gz,fastq,1477268521.0,19562904.0,GSM3449964 r1,0:75.51 1:0,A:399601730;C:333778207;G:337372866;T:406448608;N:67110,75,0,,,399601730,333778207,337372866,406448608,67110,SRX4950825,SRS3993017,SRA800291,GEO,"Center for Medical Genetics, Ghent University",1,0.90617,,0.09373,,0.74558,,0.49316,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,Belgium,2018-10-29,Larval,Larval,Undetermined,Undetermined
51961,SRR8928878,SRX5709835,SRS4649006,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 TCCTGAGC TCGACTAG control psbulk,GSM3730589,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 TCCTGAGC TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730589,GSM3730589: GC056865 TCCTGAGC TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730589,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730589,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_TCCTGAGC-TCGACTAG.R1.fastq.gz GC056865_TCCTGAGC-TCGACTAG.R2.fastq.gz,fastq fastq,444398220.0,1763485.0,GSM3730589 r1,0:126 1:126,A:119701118;C:101307242;G:100291786;T:123064017;N:34057,126,126,,,119701118,101307242,100291786,123064017,34057,SRX5709835,SRS4649006,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.89209,0.88921,0.1536,0.15422,0.79894,0.79738,0.53717,0.54281,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51962,SRR8928877,SRX5709834,SRS4649005,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 TAAGGCGA TCGACTAG control psbulk,GSM3730588,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 TAAGGCGA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730588,GSM3730588: GC056865 TAAGGCGA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730588,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730588,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_TAAGGCGA-TCGACTAG.R1.fastq.gz GC056865_TAAGGCGA-TCGACTAG.R2.fastq.gz,fastq fastq,528144372.0,2095811.0,GSM3730588 r1,0:126 1:126,A:138899905;C:124559386;G:123781108;T:140862443;N:41530,126,126,,,138899905,124559386,123781108,140862443,41530,SRX5709834,SRS4649005,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91379,0.91147,0.16599,0.16703,0.7763,0.77621,0.57465,0.57604,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51963,SRR8928876,SRX5709833,SRS4649004,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 GGAGCTAC TCGACTAG control psbulk,GSM3730587,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 GGAGCTAC TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730587,GSM3730587: GC056865 GGAGCTAC TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730587,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730587,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_GGAGCTAC-TCGACTAG.R1.fastq.gz GC056865_GGAGCTAC-TCGACTAG.R2.fastq.gz,fastq fastq,349714260.0,1387755.0,GSM3730587 r1,0:126 1:126,A:95856833;C:77706299;G:77143719;T:98982484;N:24925,126,126,,,95856833,77706299,77143719,98982484,24925,SRX5709833,SRS4649004,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91376,0.91378,0.11578,0.11732,0.82546,0.82446,0.61066,0.61085,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51964,SRR8928875,SRX5709832,SRS4649003,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 GCGTAGTA TCGACTAG control psbulk,GSM3730586,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 GCGTAGTA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730586,GSM3730586: GC056865 GCGTAGTA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730586,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730586,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_GCGTAGTA-TCGACTAG.R1.fastq.gz GC056865_GCGTAGTA-TCGACTAG.R2.fastq.gz,fastq fastq,397190556.0,1576153.0,GSM3730586 r1,0:126 1:126,A:108614389;C:88489174;G:87744396;T:112305346;N:37251,126,126,,,108614389,88489174,87744396,112305346,37251,SRX5709832,SRS4649003,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91036,0.90994,0.14864,0.15033,0.82856,0.82775,0.55841,0.55225,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51966,SRR8928873,SRX5709830,SRS4649001,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 CGTACTAG TCGACTAG control psbulk,GSM3730584,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 CGTACTAG TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730584,GSM3730584: GC056865 CGTACTAG TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730584,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730584,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_CGTACTAG-TCGACTAG.R1.fastq.gz GC056865_CGTACTAG-TCGACTAG.R2.fastq.gz,fastq fastq,357178500.0,1417375.0,GSM3730584 r1,0:126 1:126,A:95513887;C:82092508;G:81942895;T:97595862;N:33348,126,126,,,95513887,82092508,81942895,97595862,33348,SRX5709830,SRS4649001,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.91549,0.91361,0.16607,0.16725,0.79149,0.79348,0.59191,0.59784,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51967,SRR8928872,SRX5709829,SRS4649000,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 CGGAGCCT TCGACTAG control psbulk,GSM3730583,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 CGGAGCCT TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730583,GSM3730583: GC056865 CGGAGCCT TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730583,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730583,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_CGGAGCCT-TCGACTAG.R1.fastq.gz GC056865_CGGAGCCT-TCGACTAG.R2.fastq.gz,fastq fastq,382960620.0,1519685.0,GSM3730583 r1,0:126 1:126,A:103791762;C:86709889;G:85905860;T:106521094;N:32015,126,126,,,103791762,86709889,85905860,106521094,32015,SRX5709829,SRS4649000,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.92265,0.92161,0.10837,0.10936,0.81619,0.81653,0.55235,0.53794,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51969,SRR8928870,SRX5709827,SRS4648998,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 AGGCAGAA TCGACTAG control psbulk,GSM3730581,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 AGGCAGAA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730581,GSM3730581: GC056865 AGGCAGAA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730581,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730581,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_AGGCAGAA-TCGACTAG.R1.fastq.gz GC056865_AGGCAGAA-TCGACTAG.R2.fastq.gz,fastq fastq,552338892.0,2191821.0,GSM3730581 r1,0:126 1:126,A:147583784;C:127503198;G:126780271;T:150428519;N:43120,126,126,,,147583784,127503198,126780271,150428519,43120,SRX5709827,SRS4648998,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.92013,0.91808,0.11656,0.11807,0.82148,0.82181,0.55295,0.5503,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51971,SRR8928868,SRX5709825,SRS4648996,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056865 ACTCGCTA TCGACTAG control psbulk,GSM3730579,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056865 ACTCGCTA TCGACTAG control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730579,GSM3730579: GC056865 ACTCGCTA TCGACTAG control psbulk; Danio rerio; RNA Seq,GSM3730579,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730579,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056865_ACTCGCTA-TCGACTAG.R1.fastq.gz GC056865_ACTCGCTA-TCGACTAG.R2.fastq.gz,fastq fastq,349502076.0,1386913.0,GSM3730579 r1,0:126 1:126,A:95872070;C:77657456;G:76918048;T:99026360;N:28142,126,126,,,95872070,77657456,76918048,99026360,28142,SRX5709825,SRS4648996,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.90596,0.90497,0.17112,0.17311,0.80275,0.80273,0.61121,0.6138,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51974,SRR8928865,SRX5709822,SRS4648993,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056829 TAAGGCGA CTCTCTAT control psbulk,GSM3730576,,source name:mitfa:GFP cells from control|tissue:GFP+ cells from control,GC056829 TAAGGCGA CTCTCTAT control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,tissue:GFP+ cells from control,GSM3730576,GSM3730576: GC056829 TAAGGCGA CTCTCTAT control psbulk; Danio rerio; RNA Seq,GSM3730576,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730576,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056829_TAAGGCGA-CTCTCTAT.R1.fastq.gz GC056829_TAAGGCGA-CTCTCTAT.R2.fastq.gz,fastq fastq,99705564.0,395657.0,GSM3730576 r1,0:126 1:126,A:26405998;C:23306835;G:22991686;T:26965397;N:35648,126,126,,,26405998,23306835,22991686,26965397,35648,SRX5709822,SRS4648993,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.88077,0.88005,0.07214,0.07291,0.82885,0.8283,0.55221,0.55358,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
51977,SRR8928862,SRX5709819,SRS4648990,SRP193005,PRJNA533623,MITF low zebrafish melanomas reveal cells with no MITF activity at the site of residual disease,GSE130037,Transcriptome Analysis,The MITF low melanoma transcriptional signature is predictive of poor outcome for patients but little is known about its biological signature. We used genetic models of zebrafish with low expression of mitfa MITF low to study this biological subtype. We performed whole bulk RNA seq to classify zebrafish MITF low melanoma that cluster mainly by their directionality of growth and assess their resemblance to patients' MITF low subgroups. Furthermore  using genetic inhibition of MITF activity we discover minimal residual disease at the site of regression and using single cell and low input RNA seq we characterise these MITF independent cells and show that they pre exist in the primary tumour. Overall design: We performed bulk RNAseq experiment of zebrafish primary melanomas to compare different phenotypes based on directionality of growth or original mutations. Further we performed single cell RNAseq of primary and regressed melanoma.,,pubmed:31582381,,GC056829 CGTACTAG CTCTCTAT control psbulk,GSM3730573,,source name:mitfa:GFP cells from control|genotype:mitfavc7|tissue:GFP+ cells from control,GC056829 CGTACTAG CTCTCTAT control psbulk,Sequence quality was checked using FastQC version 0.11.4. Raw reads were trimmed  using Cutadapt to remove Smart Seq2 adaptor sequences. The trimmed reads were mapped using STAR to the reference genome version GRCz11 Ensembl V92  20178 including coding sequences for EGFP and hsBRAFV600E and point mutations in p53 and mitfa. Aligned reads were quantified using Salmon in the alignment based mode. Illumina  software used for basecalling. Sequence quality was checked using FastQC version 0.11.3 Reads were aligned to the zebrafish genome GRCz11 using STAR STAR 2.5.1b with the default parameters or using Salmon in the alignment based mode The quality of the resulting alignment to the transcriptome Ensembl annotation version GRCz11 has been checked using RNASeqQC v1.1.8.1 Raw counts of reads covering the transcriptome Ensembl annotation version GRCz11 was obtained using htseq count 0.6.1 with the “ s reverse” option. Genome build: Zebrafish GRCz11 Supplementary files format and content: tab delimited filed of raw counts at gene level for each sample,mitfa:GFP cells from control,,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,,genotype:mitfavc7|tissue:GFP+ cells from control,GSM3730573,GSM3730573: GC056829 CGTACTAG CTCTCTAT control psbulk; Danio rerio; RNA Seq,GSM3730573,,1,FACS sorting of 50 GFP+ living cells from control  SMARTseq2 Picelli et al 2014 polyA selection cDNA   TruSeq or Nextera XT RNA Seq  Paired end reads,GEO Accession:GSM3730573,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP193005,,,GC056829_CGTACTAG-CTCTCTAT.R1.fastq.gz GC056829_CGTACTAG-CTCTCTAT.R2.fastq.gz,fastq fastq,160942320.0,638660.0,GSM3730573 r1,0:126 1:126,A:41566703;C:39183347;G:38725528;T:41411306;N:55436,126,126,,,41566703,39183347,38725528,41411306,55436,SRX5709819,SRS4648990,SRA876955,GEO,"Prof. Patton lab, MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit & Cancer Research UK EC",2,0.94263,0.9412,0.04967,0.04955,0.823,0.82242,0.5265,0.53254,126,126,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2019-04-18,Undetermined,Undetermined,Undetermined,Undetermined
68913,SRR18220751,SRX14367197,SRS12180292,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mp rep 4,GSM5934077,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,YAP.Mp rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934077,GSM5934077: YAP.Mp rep 4; Danio rerio; RNA Seq,GSM5934077 r1,GSM5934077,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3653.fq.gz,fastq,328872760.0,8221819.0,GSM5934077 r1,0:40,A:90948230;C:73452026;G:74032280;T:90413909;N:26315,40,,,,90948230,73452026,74032280,90413909,26315,SRX14367197,SRS12180292,SRA1380881,Koch Institute,Koch Institute,1,0.90618,,0.10438,,0.72821,,0.5118,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68914,SRR18220752,SRX14367196,SRS12180291,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mp rep 3,GSM5934076,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,YAP.Mp rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934076,GSM5934076: YAP.Mp rep 3; Danio rerio; RNA Seq,GSM5934076 r1,GSM5934076,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3652.fq.gz,fastq,206954000.0,5173850.0,GSM5934076 r1,0:40,A:52606897;C:50606914;G:50994533;T:52729555;N:16101,40,,,,52606897,50606914,50994533,52729555,16101,SRX14367196,SRS12180291,SRA1380881,Koch Institute,Koch Institute,1,0.93105,,0.06578,,0.71965,,0.5059,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68915,SRR18220753,SRX14367195,SRS12180290,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mp rep 2,GSM5934075,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,YAP.Mp rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934075,GSM5934075: YAP.Mp rep 2; Danio rerio; RNA Seq,GSM5934075 r1,GSM5934075,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3651.fq.gz,fastq,294999240.0,7374981.0,GSM5934075 r1,0:40,A:73485008;C:72954412;G:73986972;T:74549836;N:23012,40,,,,73485008,72954412,73986972,74549836,23012,SRX14367195,SRS12180290,SRA1380881,Koch Institute,Koch Institute,1,0.92301,,0.05942,,0.71956,,0.50344,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68916,SRR18220754,SRX14367194,SRS12180289,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mp rep 1,GSM5934074,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,YAP.Mp rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934074,GSM5934074: YAP.Mp rep 1; Danio rerio; RNA Seq,GSM5934074 r1,GSM5934074,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3650.fq.gz,fastq,335618840.0,8390471.0,GSM5934074 r1,0:40,A:101815451;C:65811220;G:66968247;T:100997604;N:26318,40,,,,101815451,65811220,66968247,100997604,26318,SRX14367194,SRS12180289,SRA1380881,Koch Institute,Koch Institute,1,0.89759,,0.13185,,0.72888,,0.58031,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68917,SRR18220755,SRX14367193,SRS12180288,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mm rep 4,GSM5934073,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,YAP.Mm rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934073,GSM5934073: YAP.Mm rep 4; Danio rerio; RNA Seq,GSM5934073 r1,GSM5934073,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3657.fq.gz,fastq,505578840.0,12639471.0,GSM5934073 r1,0:40,A:151358215;C:100212599;G:101677867;T:152291228;N:38931,40,,,,151358215,100212599,101677867,152291228,38931,SRX14367193,SRS12180288,SRA1380881,Koch Institute,Koch Institute,1,0.88348,,0.15567,,0.73016,,0.54726,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68918,SRR18220756,SRX14367192,SRS12180287,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mm rep 3,GSM5934072,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,YAP.Mm rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934072,GSM5934072: YAP.Mm rep 3; Danio rerio; RNA Seq,GSM5934072 r1,GSM5934072,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3656.fq.gz,fastq,525665000.0,13141625.0,GSM5934072 r1,0:40,A:157287064;C:104222026;G:104521836;T:159593407;N:40667,40,,,,157287064,104222026,104521836,159593407,40667,SRX14367192,SRS12180287,SRA1380881,Koch Institute,Koch Institute,1,0.86627,,0.15858,,0.74024,,0.55114,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68919,SRR18220757,SRX14367191,SRS12180286,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mm rep 2,GSM5934071,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,YAP.Mm rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934071,GSM5934071: YAP.Mm rep 2; Danio rerio; RNA Seq,GSM5934071 r1,GSM5934071,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3655.fq.gz,fastq,656843160.0,16421079.0,GSM5934071 r1,0:40,A:198634504;C:128192658;G:129776729;T:200187591;N:51678,40,,,,198634504,128192658,129776729,200187591,51678,SRX14367191,SRS12180286,SRA1380881,Koch Institute,Koch Institute,1,0.86932,,0.13652,,0.74079,,0.5049,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68920,SRR18220758,SRX14367190,SRS12180285,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,YAP.Mm rep 1,GSM5934070,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,YAP.Mm rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:YAP S127A S381A;mitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934070,GSM5934070: YAP.Mm rep 1; Danio rerio; RNA Seq,GSM5934070 r1,GSM5934070,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3654.fq.gz,fastq,178362520.0,4459063.0,GSM5934070 r1,0:40,A:51803050;C:37429443;G:38208586;T:50907455;N:13986,40,,,,51803050,37429443,38208586,50907455,13986,SRX14367190,SRS12180285,SRA1380881,Koch Institute,Koch Institute,1,0.8844,,0.10339,,0.74048,,0.56556,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68921,SRR18220759,SRX14367189,SRS12180284,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mp rep 4,GSM5934069,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,Q.Mp rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934069,GSM5934069: Q.Mp rep 4; Danio rerio; RNA Seq,GSM5934069 r1,GSM5934069,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3645.fq.gz,fastq,439470600.0,10986765.0,GSM5934069 r1,0:40,A:123070962;C:96298442;G:97520777;T:122545555;N:34864,40,,,,123070962,96298442,97520777,122545555,34864,SRX14367189,SRS12180284,SRA1380881,Koch Institute,Koch Institute,1,0.90571,,0.1028,,0.72857,,0.54701,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68922,SRR18220760,SRX14367188,SRS12180283,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mp rep 3,GSM5934068,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,Q.Mp rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934068,GSM5934068: Q.Mp rep 3; Danio rerio; RNA Seq,GSM5934068 r1,GSM5934068,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3644.fq.gz,fastq,194824680.0,4870617.0,GSM5934068 r1,0:40,A:50412635;C:46659956;G:47372769;T:50364066;N:15254,40,,,,50412635,46659956,47372769,50364066,15254,SRX14367188,SRS12180283,SRA1380881,Koch Institute,Koch Institute,1,0.91462,,0.06516,,0.73018,,0.52258,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68923,SRR18220761,SRX14367187,SRS12180282,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mp rep 2,GSM5934067,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,Q.Mp rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934067,GSM5934067: Q.Mp rep 2; Danio rerio; RNA Seq,GSM5934067 r1,GSM5934067,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3643.fq.gz,fastq,306202040.0,7655051.0,GSM5934067 r1,0:40,A:76615531;C:75566901;G:76566888;T:77429291;N:23429,40,,,,76615531,75566901,76566888,77429291,23429,SRX14367187,SRS12180282,SRA1380881,Koch Institute,Koch Institute,1,0.92524,,0.05546,,0.73371,,0.53446,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68924,SRR18220762,SRX14367186,SRS12180281,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mp rep 1,GSM5934066,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,Q.Mp rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934066,GSM5934066: Q.Mp rep 1; Danio rerio; RNA Seq,GSM5934066 r1,GSM5934066,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3642.fq.gz,fastq,199449760.0,4986244.0,GSM5934066 r1,0:40,A:50476027;C:48887666;G:49450276;T:50619972;N:15819,40,,,,50476027,48887666,49450276,50619972,15819,SRX14367186,SRS12180281,SRA1380881,Koch Institute,Koch Institute,1,0.93339,,0.06306,,0.72689,,0.52289,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68925,SRR18220763,SRX14367185,SRS12180280,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mm rep 4,GSM5934065,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,Q.Mm rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934065,GSM5934065: Q.Mm rep 4; Danio rerio; RNA Seq,GSM5934065 r1,GSM5934065,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3649.fq.gz,fastq,480171400.0,12004285.0,GSM5934065 r1,0:40,A:147506754;C:91596477;G:93536128;T:147493879;N:38162,40,,,,147506754,91596477,93536128,147493879,38162,SRX14367185,SRS12180280,SRA1380881,Koch Institute,Koch Institute,1,0.87342,,0.14605,,0.73827,,0.56348,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68926,SRR18220764,SRX14367184,SRS12180279,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mm rep 3,GSM5934064,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,Q.Mm rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934064,GSM5934064: Q.Mm rep 3; Danio rerio; RNA Seq,GSM5934064 r1,GSM5934064,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3648.fq.gz,fastq,575951800.0,14398795.0,GSM5934064 r1,0:40,A:174656165;C:111845103;G:113188796;T:176216000;N:45736,40,,,,174656165,111845103,113188796,176216000,45736,SRX14367184,SRS12180279,SRA1380881,Koch Institute,Koch Institute,1,0.87465,,0.15269,,0.73401,,0.56404,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68927,SRR18220765,SRX14367183,SRS12180278,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mm rep 2,GSM5934063,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,Q.Mm rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934063,GSM5934063: Q.Mm rep 2; Danio rerio; RNA Seq,GSM5934063 r1,GSM5934063,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3647.fq.gz,fastq,638608160.0,15965204.0,GSM5934063 r1,0:40,A:195927745;C:122976947;G:124896005;T:194757488;N:49975,40,,,,195927745,122976947,124896005,194757488,49975,SRX14367183,SRS12180278,SRA1380881,Koch Institute,Koch Institute,1,0.87559,,0.1492,,0.74489,,0.49976,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68928,SRR18220766,SRX14367182,SRS12180277,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,Q.Mm rep 1,GSM5934062,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,Q.Mm rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:GNAQ Q209L;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934062,GSM5934062: Q.Mm rep 1; Danio rerio; RNA Seq,GSM5934062 r1,GSM5934062,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3646.fq.gz,fastq,172383440.0,4309586.0,GSM5934062 r1,0:40,A:51651269;C:34403021;G:35088400;T:51227042;N:13708,40,,,,51651269,34403021,35088400,51227042,13708,SRX14367182,SRS12180277,SRA1380881,Koch Institute,Koch Institute,1,0.89084,,0.12537,,0.73141,,0.4843,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68929,SRR18220767,SRX14367181,SRS12180276,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mp rep 4,GSM5934061,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,p53.Mp rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934061,GSM5934061: p53.Mp rep 4; Danio rerio; RNA Seq,GSM5934061 r1,GSM5934061,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3638.fq.gz,fastq,107430560.0,2685764.0,GSM5934061 r1,0:40,A:26974706;C:26530640;G:26771595;T:27145328;N:8291,40,,,,26974706,26530640,26771595,27145328,8291,SRX14367181,SRS12180276,SRA1380881,Koch Institute,Koch Institute,1,0.93538,,0.05953,,0.72074,,0.49298,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68930,SRR18220768,SRX14367180,SRS12180275,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mp rep 3,GSM5934060,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,p53.Mp rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934060,GSM5934060: p53.Mp rep 3; Danio rerio; RNA Seq,GSM5934060 r1,GSM5934060,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3637.fq.gz,fastq,291457000.0,7286425.0,GSM5934060 r1,0:40,A:72423033;C:72725590;G:73478939;T:72806465;N:22973,40,,,,72423033,72725590,73478939,72806465,22973,SRX14367180,SRS12180275,SRA1380881,Koch Institute,Koch Institute,1,0.93351,,0.05363,,0.72573,,0.50875,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68931,SRR18220769,SRX14367179,SRS12180274,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mp rep 2,GSM5934059,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,p53.Mp rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934059,GSM5934059: p53.Mp rep 2; Danio rerio; RNA Seq,GSM5934059 r1,GSM5934059,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3636.fq.gz,fastq,188554400.0,4713860.0,GSM5934059 r1,0:40,A:46655155;C:47293713;G:47769597;T:46820972;N:14963,40,,,,46655155,47293713,47769597,46820972,14963,SRX14367179,SRS12180274,SRA1380881,Koch Institute,Koch Institute,1,0.93778,,0.04944,,0.71376,,0.49096,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68932,SRR18220770,SRX14367178,SRS12180273,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mp rep 1,GSM5934058,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,p53.Mp rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa; half tp53 M214K/+  half tp53 +/+,GSM5934058,GSM5934058: p53.Mp rep 1; Danio rerio; RNA Seq,GSM5934058 r1,GSM5934058,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3635.fq.gz,fastq,350895800.0,8772395.0,GSM5934058 r1,0:40,A:89658505;C:84530000;G:85487507;T:91192464;N:27324,40,,,,89658505,84530000,85487507,91192464,27324,SRX14367178,SRS12180273,SRA1380881,Koch Institute,Koch Institute,1,0.91223,,0.07333,,0.71273,,0.50505,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68933,SRR18220771,SRX14367177,SRS12180272,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mm rep 3,GSM5934057,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,p53.Mm rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934057,GSM5934057: p53.Mm rep 3; Danio rerio; RNA Seq,GSM5934057 r1,GSM5934057,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3641.fq.gz,fastq,288420480.0,7210512.0,GSM5934057 r1,0:40,A:75129840;C:68495689;G:69439498;T:75332621;N:22832,40,,,,75129840,68495689,69439498,75332621,22832,SRX14367177,SRS12180272,SRA1380881,Koch Institute,Koch Institute,1,0.92216,,0.0803,,0.71474,,0.4986,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68934,SRR18220772,SRX14367176,SRS12180271,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mm rep 2,GSM5934056,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,p53.Mm rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934056,GSM5934056: p53.Mm rep 2; Danio rerio; RNA Seq,GSM5934056 r1,GSM5934056,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3640.fq.gz,fastq,433372320.0,10834308.0,GSM5934056 r1,0:40,A:124541346;C:92199450;G:93724266;T:122873275;N:33983,40,,,,124541346,92199450,93724266,122873275,33983,SRX14367176,SRS12180271,SRA1380881,Koch Institute,Koch Institute,1,0.89727,,0.11246,,0.72679,,0.54608,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68935,SRR18220773,SRX14367175,SRS12180270,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,p53.Mm rep 1,GSM5934055,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,p53.Mm rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2; half tp53 M214K/+  half tp53 +/+,GSM5934055,GSM5934055: p53.Mm rep 1; Danio rerio; RNA Seq,GSM5934055 r1,GSM5934055,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3639.fq.gz,fastq,645871960.0,16146799.0,GSM5934055 r1,0:40,A:185012715;C:137405354;G:139229035;T:184173751;N:51105,40,,,,185012715,137405354,139229035,184173751,51105,SRX14367175,SRS12180270,SRA1380881,Koch Institute,Koch Institute,1,0.8997,,0.12259,,0.726,,0.54234,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68936,SRR18220774,SRX14367174,SRS12180269,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mp rep 3,GSM5934054,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,NTG.Mp rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934054,GSM5934054: NTG.Mp rep 3; Danio rerio; RNA Seq,GSM5934054 r1,GSM5934054,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3630.fq.gz,fastq,99649120.0,2491228.0,GSM5934054 r1,0:40,A:24853387;C:24769504;G:25058685;T:24959630;N:7914,40,,,,24853387,24769504,25058685,24959630,7914,SRX14367174,SRS12180269,SRA1380881,Koch Institute,Koch Institute,1,0.93728,,0.06004,,0.71928,,0.49976,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68937,SRR18220775,SRX14367173,SRS12180268,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mp rep 2,GSM5934053,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,NTG.Mp rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934053,GSM5934053: NTG.Mp rep 2; Danio rerio; RNA Seq,GSM5934053 r1,GSM5934053,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3629.fq.gz,fastq,143382080.0,3584552.0,GSM5934053 r1,0:40,A:35218709;C:36186045;G:36543446;T:35422532;N:11348,40,,,,35218709,36186045,36543446,35422532,11348,SRX14367173,SRS12180268,SRA1380881,Koch Institute,Koch Institute,1,0.93741,,0.04311,,0.72245,,0.51347,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68938,SRR18220776,SRX14367172,SRS12180267,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mp rep 1,GSM5934052,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,NTG.Mp rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934052,GSM5934052: NTG.Mp rep 1; Danio rerio; RNA Seq,GSM5934052 r1,GSM5934052,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3628.fq.gz,fastq,226497120.0,5662428.0,GSM5934052 r1,0:40,A:56128467;C:56636405;G:57225146;T:56489383;N:17719,40,,,,56128467,56636405,57225146,56489383,17719,SRX14367172,SRS12180267,SRA1380881,Koch Institute,Koch Institute,1,0.93328,,0.05449,,0.71313,,0.51655,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68939,SRR18220777,SRX14367171,SRS12180266,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mm rep 4,GSM5934051,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,NTG.Mm rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934051,GSM5934051: NTG.Mm rep 4; Danio rerio; RNA Seq,GSM5934051 r1,GSM5934051,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3634.fq.gz,fastq,185309440.0,4632736.0,GSM5934051 r1,0:40,A:45876166;C:46365034;G:46900623;T:46153546;N:14071,40,,,,45876166,46365034,46900623,46153546,14071,SRX14367171,SRS12180266,SRA1380881,Koch Institute,Koch Institute,1,0.93405,,0.05991,,0.72032,,0.50856,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68940,SRR18220778,SRX14367170,SRS12180265,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mm rep 3,GSM5934050,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,NTG.Mm rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934050,GSM5934050: NTG.Mm rep 3; Danio rerio; RNA Seq,GSM5934050 r1,GSM5934050,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3633.fq.gz,fastq,272430200.0,6810755.0,GSM5934050 r1,0:40,A:68173356;C:67403161;G:68278936;T:68553503;N:21244,40,,,,68173356,67403161,68278936,68553503,21244,SRX14367170,SRS12180265,SRA1380881,Koch Institute,Koch Institute,1,0.93068,,0.05429,,0.726,,0.51647,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68941,SRR18220779,SRX14367169,SRS12180264,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mm rep 2,GSM5934049,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,NTG.Mm rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934049,GSM5934049: NTG.Mm rep 2; Danio rerio; RNA Seq,GSM5934049 r1,GSM5934049,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3632.fq.gz,fastq,279066200.0,6976655.0,GSM5934049 r1,0:40,A:71052970;C:67989605;G:68663741;T:71338060;N:21824,40,,,,71052970,67989605,68663741,71338060,21824,SRX14367169,SRS12180264,SRA1380881,Koch Institute,Koch Institute,1,0.92601,,0.06622,,0.7231,,0.51715,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68942,SRR18220780,SRX14367168,SRS12180263,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,NTG.Mm rep 1,GSM5934048,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,NTG.Mm rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934048,GSM5934048: NTG.Mm rep 1; Danio rerio; RNA Seq,GSM5934048 r1,GSM5934048,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3631.fq.gz,fastq,397511480.0,9937787.0,GSM5934048 r1,0:40,A:99537869;C:98366312;G:99436392;T:100139360;N:31547,40,,,,99537869,98366312,99436392,100139360,31547,SRX14367168,SRS12180263,SRA1380881,Koch Institute,Koch Institute,1,0.9301,,0.05912,,0.72531,,0.50285,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68943,SRR18220781,SRX14367167,SRS12180262,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mp rep 4,GSM5934047,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,BRAF.Mp rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934047,GSM5934047: BRAF.Mp rep 4; Danio rerio; RNA Seq,GSM5934047 r1,GSM5934047,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3661.fq.gz,fastq,377051960.0,9426299.0,GSM5934047 r1,0:40,A:110376838;C:77899765;G:78244559;T:110501518;N:29280,40,,,,110376838,77899765,78244559,110501518,29280,SRX14367167,SRS12180262,SRA1380881,Koch Institute,Koch Institute,1,0.90498,,0.14711,,0.74795,,0.55862,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68944,SRR18220782,SRX14367166,SRS12180261,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mp rep 3,GSM5934046,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,BRAF.Mp rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934046,GSM5934046: BRAF.Mp rep 3; Danio rerio; RNA Seq,GSM5934046 r1,GSM5934046,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3660.fq.gz,fastq,328971080.0,8224277.0,GSM5934046 r1,0:40,A:92658466;C:71538587;G:72091486;T:92656916;N:25625,40,,,,92658466,71538587,72091486,92656916,25625,SRX14367166,SRS12180261,SRA1380881,Koch Institute,Koch Institute,1,0.91119,,0.12419,,0.74286,,0.53286,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68945,SRR18220783,SRX14367165,SRS12180260,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mp rep 1,GSM5934045,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,BRAF.Mp rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:wild type mitfa,GSM5934045,GSM5934045: BRAF.Mp rep 1; Danio rerio; RNA Seq,GSM5934045 r1,GSM5934045,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3658.fq.gz,fastq,380112720.0,9502818.0,GSM5934045 r1,0:40,A:113182889;C:76450216;G:76796048;T:113653793;N:29774,40,,,,113182889,76450216,76796048,113653793,29774,SRX14367165,SRS12180260,SRA1380881,Koch Institute,Koch Institute,1,0.89838,,0.15924,,0.73687,,0.55351,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68946,SRR18220784,SRX14367164,SRS12180259,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mm rep 4,GSM5934044,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,BRAF.Mm rep 4,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934044,GSM5934044: BRAF.Mm rep 4; Danio rerio; RNA Seq,GSM5934044 r1,GSM5934044,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3665.fq.gz,fastq,463802640.0,11595066.0,GSM5934044 r1,0:40,A:137205138;C:93744923;G:94009928;T:138806446;N:36205,40,,,,137205138,93744923,94009928,138806446,36205,SRX14367164,SRS12180259,SRA1380881,Koch Institute,Koch Institute,1,0.88527,,0.14212,,0.72212,,0.53223,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68947,SRR18220785,SRX14367163,SRS12180258,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mm rep 3,GSM5934043,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,BRAF.Mm rep 3,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934043,GSM5934043: BRAF.Mm rep 3; Danio rerio; RNA Seq,GSM5934043 r1,GSM5934043,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3664.fq.gz,fastq,530639840.0,13265996.0,GSM5934043 r1,0:40,A:158116112;C:106342247;G:106149806;T:159989924;N:41751,40,,,,158116112,106342247,106149806,159989924,41751,SRX14367163,SRS12180258,SRA1380881,Koch Institute,Koch Institute,1,0.88779,,0.15994,,0.71025,,0.51088,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68948,SRR18220786,SRX14367162,SRS12180257,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mm rep 2,GSM5934042,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,BRAF.Mm rep 2,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934042,GSM5934042: BRAF.Mm rep 2; Danio rerio; RNA Seq,GSM5934042 r1,GSM5934042,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3663.fq.gz,fastq,667063480.0,16676587.0,GSM5934042 r1,0:40,A:200306865;C:131864026;G:131763140;T:203076669;N:52780,40,,,,200306865,131864026,131763140,203076669,52780,SRX14367162,SRS12180257,SRA1380881,Koch Institute,Koch Institute,1,0.87289,,0.14746,,0.72541,,0.52837,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined
68949,SRR18220787,SRX14367161,SRS12180256,SRP362487,PRJNA812890,MITF deficiency and oncogenic GNAQ each promote proliferation programs in zebrafish melanocyte lineage cells,GSE197927,Transcriptome Analysis,Uveal melanoma UM is the most common primary malignancy of the eye in adults  but lacks any FDA approved therapy for the deadly metastatic disease. Thus  there is great need to dissect the driving mechanisms for UM  and develop strategies to evaluate potential therapeutics. Using a zebrafish model  we previously identified MITF  the master melanocyte transcription factor  as a tumor suppressor in GNAQQ209L driven UM. Here  we show that zebrafish mitfa deficient GNAQQ209L driven tumors significantly up regulate neural crest markers  and higher expression of a melanoma associated neural crest signature correlates with poor UM patient survival. We further determined how the mitfa null state  as well as expression of GNAQQ209L  YAPS127A;S381A  or BRAFV600E oncogenes  impacts melanocyte lineage cells before they acquire the transformed state. Specifically  examination 5 dpf showed that mitfa deficiency is sufficient to upregulate pigment progenitor and neural crest markers  while GNAQQ209L expression promotes a proliferative phenotype that is further enhanced by YAPS127A;S381A co expression. Finally  we show that this oncogene induced proliferative phenotype can be used to screen chemical inhibitors for their efficacy against the UM pathway. Overall  this study establishes that a neural crest signature correlates with poor UM survival  and describes an in vivo assay for pre clinical trials of potential UM therapeutics. Overall design: Four replicates each of 5 dpf larval cells expressing a mitfa:GFP reporter on wild type and null mitfa backgrounds compared to similar groups with added BRAF  GNAQ and YAP transgenes.,,pubmed:35869673,,BRAF.Mm rep 1,GSM5934041,,tissue:cells isolated from 5 dpf larvae that express a mitfa:GFP reporter|genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,BRAF.Mm rep 1,HiSeq 2000 using v3 chemistry. Software: Control v2.2.58  RTA 1.18.64. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch. RNA seq data was used to quantify transcripts from the zv11 zebrafish assembly with the Ensembl version 104 annotation using Salmon version 1.3.0 Patro et al. 2017. Gene level summaries were prepared using tximport version 1.20.0 Soneson  Love  and Robinson 2015 running under R version 4.1.0 R Core Team 2021. Genome build: zv11 with an ensembl version 104 annotation Supplementary files format and content: gphelps intCt.txt.gz is a tab delimited text file of integer count data Supplementary files format and content: gphelps l2tpm.txt.gz is a tab delimited text file of log2 counts per million with a plus 1 offset,cells isolated from 5 dpf larvae that express a mitfa:GFP reporter,Zebrafish 5 dpf larvae 100 1 000 per sample were anesthetized in 0.1% tricaine.,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,genetic background:AB/Tubingen TAB5/14|transgene:Tgmitfa:BRAF V600E;Tgmitfa:EGFP|genotype:mitfa null w2/w2,GSM5934041,GSM5934041: BRAF.Mm rep 1; Danio rerio; RNA Seq,GSM5934041 r1,GSM5934041,1,RNeasy Micro Kit Qiagen Samples were analyzed for RNA integrity using a Femto Analyzer  and samples with a RIN > 8 were submitted for library prep. cDNA was prepared from 1uL of total RNA using the SMART Seq v4 Ultra Low Input RNA Kit Takara using 14 cycles of amplification. Resulting cDNA were confirmed using a Fragment Analyzer and Illumina libraries prepared using NexteraXT Illumina and sequenced on a HiSeq2000 Illumina using 40nt single end reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP362487,,,d3662.fq.gz,fastq,247368640.0,6184216.0,GSM5934041 r1,0:40,A:73341034;C:50031128;G:50973285;T:73003869;N:19324,40,,,,73341034,50031128,50973285,73003869,19324,SRX14367161,SRS12180256,SRA1380881,Koch Institute,Koch Institute,1,0.89039,,0.13845,,0.74272,,0.50233,,40,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Unknown,2022-03-04,Larval,Larval,Undetermined,Undetermined