run_metadata: 32852

This data as json

rowid	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	tech_variant	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
32852	SRR29482331	SRX24993377	SRS21694841	SRP515141	PRJNA1126244	Specific oncogene activation of the cell of origin in mucosal melanoma [RNA Seq]	GSE270354	Transcriptome Analysis	Mucosal melanoma MM is a deadly cancer derived from mucosal melanocytes. To test the consequences of MM genetics we develop a zebrafish model in which all melanocytes experience CCND1 expression and loss of PTEN and TP53. Surprisingly melanoma only develops from melanocytes lining internal organs analogous to the location of patient MM. We find that zebrafish MMs have a unique chromatin landscape from cutaneous melanoma. Internal melanocytes are labeled using a MM specific transcriptional enhancer. Normal zebrafish internal melanocytes share a gene expression signature with MMs. Patient and zebrafish MMs show increased migratory neural crest gene and decreased antigen presentation gene expression consistent with the increased metastatic behavior and decreased immunotherapy sensitivity of MM. Our work suggests the cell state of the originating melanocyte influences the behavior of derived melanomas. Our animal model phenotypically and transcriptionally mimics patient tumors allowing this model to be used for MM therapeutic discovery. As this is a non MAPK driven genetically engineered model of melanoma our work also has implications for the 15% of cutaneous melanoma patients who lack MAPK driving mutations. Overall design: Bulk RNA sequencing data from mucosal melanoma and cutaneous melanoma zebrafish models				MM rep3 [RNA Seq]	GSM8340233		source name:mucosal melanoma\|tissue:mucosal melanoma\|cell type:melanoma\|genotype:roy / ; mitfa / fish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1\|geo loc name:missing\|collection date:missing	MM rep3 [RNA Seq]	Cutadpt was used to remove adaptor sequences and low quality regions. The high quality reads were aligned to UCSC build danRer11 of zebrafish genome using Tophat 2.0.11 without xxx splicing form calls. Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. Assembly: danRer11 Supplementary files format and content: .txt file contains differential gene expression of mucosal melanoma samples vs. cutaneous melanoma	mucosal melanoma		Tissue was disrupted using QIAshredder columns Qiagen 79656. DNA was removed and RNA was purified using columns Qiagen 74134. RNA was polyA selected NEB E7490. NEBNext Ultra RNA Library Prep Kit for Illumina NEB E7530	Melanomas generated from mitfa / ; tp53 / ; BRAFV600E zebrafish injected with MCR:EGFP or roy / ; mitfa / zebrafish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1were isolated for RNA seq.	tissue:mucosal melanoma\|cell type:melanoma\|genotype:roy / ; mitfa / fish injected with CRISPR MCR:tp53 sgRNA; CRISPR MCR:ptena/b sgRNA; MCR:CCND1	GSM8340233	GSM8340233: MM rep3 [RNA Seq]; Danio rerio; RNA Seq	GSM8340233 r1	GSM8340233	1	Tissue was disrupted using QIAshredder columns Qiagen 79656. DNA was removed and RNA was purified using columns Qiagen 74134. RNA was polyA selected NEB E7490. NEBNext Ultra RNA Library Prep Kit for Illumina NEB E7530		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP515141			MI-Dr-F379.R1.fastq.gz MI-Dr-F379.R2.fastq.gz	fastq fastq	19584405300.0	65281351.0	GSM8340233 r1	0:150 1:150	A:5193657176;C:4586793253;G:4681119346;T:5119062192;N:3773333	150	150			5193657176	4586793253	4681119346	5119062192	3773333	SRX24993377	SRS21694841	SRA1904140	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	Insco Lab, Medical Oncology, Dana Farber Cancer Institute	2	0.91009	0.91075	0.05605	0.05603	0.70709	0.71553	0.48633	0.5046	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	nebnext	bulk	bulk	bulk		United States	2024-06-20	Undetermined	Undetermined	Cancer or Tumor	Cancer or Tumor