metadata: run_metadata: 39 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue

39 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation = "Undetermined"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	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.study_ref	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.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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
50533	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	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
68913	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;