run_metadata: 68984

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
68984	SRR18278284	SRX14416134	SRS12225412	SRP363191	PRJNA814235	Profiling the cancer prone microenvironment in a zebrafish model for MPNST	GSE198220	Transcriptome Analysis	Microenvironmental contributions to soft tissue sarcoma progression are relatively undefined particularly in the context of sarcoma onset. Use of animal models to reveal these contributions is impeded by 1 the difficulty in discriminating between microenvironmental precancerous and cancer cells; and 2 the challenge in defining a precancerous microenvironment. We developed a zebrafish model that allows segregation of microenvironmental precancerous and cancerous cell populations by fluorescence activated cell sorting. This model exhibits high predilection for malignant peripheral nerve sheath tumor MPNST a type of soft tissue sarcoma that exhibits rapid aggressive growth. Using RNA seq we profiled the transcriptomes of microenvironmental cells from our zebrafish MPNST model. We show broad activation of inflammatory and immune associated signaling networks and significant upregulation of tumor promoting ligands in both precancerous and cancerous microenvironments. We also identify specific ligand receptor pairs that may promote sarcomagenesis. This work provides insight into how the microenvironment may promote MPNST initiation and progression. Overall design: N = 3 4 SAMPLES PER TREATMENT GROUP: Pre Cancerous Sox10 High Pre Cancerous Sox10 Low Control Sox10 Low Cancer Sox10 High Cancer Sox10 Low				Pre Cancerous Sox10 Low rep1	GSM5941028		source name:PreC Sox10 Low\|strain:tgsox10:RFP; brca2hg5/hg5; tp53zdf1/zdf1\|tissue:Precancerous Microenvironment\|age:4.5 months\|treatment:Sox10 Low\|geo loc name:missing\|collection date:missing	Pre Cancerous Sox10 Low rep1	The quality of sequenced data was assessed using fastqc application and 10 poor quality bases were trimmed from the 5’ end. The remaining good quality reads were aligned to the Zebrafish reference genome danRer10 downloaded from the Ensembl database using STAR aligner. Per gene counts of uniquely mapped reads were calculated using htseq count script from the HTSeq Python package for each replicate. Gene counts were imported to R and features with at least 2 counts in 8 or more samples were retained. Zebrafish ensemble gene IDs were mapped to unique ZF gene symbol and summed. DESeq2 was used to estimate size factors and generate normalized counts for downstream analyses as well as log2FC and adjusted pvalues for treatment comparions Assembly: danRer10 Supplementary files format and content: csv format read count	PreC Sox10 Low	Ocular tissues were removed enzymatically dissociated and processed by FACS	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended	Zebrafish housed and maintained under standard conditions	strain:tgsox10:RFP;brca2hg5/hg5;tp53zdf1/zdf1\|tissue:Precancerous Microenvironment\|age:4.5 months\|treatment:Sox10 Low	GSM5941028	GSM5941028: Pre Cancerous Sox10 Low rep1; Danio rerio; RNA Seq	GSM5941028 r1	GSM5941028	1	RNA was isolated with a QIAGEN miRneasy kit according to manufacturer directions with RNA quality assessed with Agilent Bioanalyzer RNA seq libraries were constructed using NEBNext Ultra Directional RNA Library Prep Kit and NEBNext Mulitplex Oligos for Illumina NEB. RNA seq double ended		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP363191		loader:fastq load.py	ONP1_RFPminus_S6_R2_001.fastq.gz ONP1_RFPminus_S6_R1_001.fastq.gz	fastq fastq	8449095256.0	55586153.0	GSM5941028 r1	0:76 1:76	A:2285725917;C:1928716547;G:1967054415;T:2264542755;N:3055622	76	76			2285725917	1928716547	1967054415	2264542755	3055622	SRX14416134	SRS12225412	SRA1386032	Center for Human Health and the Environment (CHHE) and Bioinformatics Research Center (BRC), North Carolina State University	CHHE, NCSU	2	0.92533	0.92685	0.14583	0.14304	0.72082	0.72466	0.5591	0.56338	76	76	B	B	biological fallback assumption	illumina	nextseq	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		United States	2022-03-09	Adult	Adult	Undetermined	Undetermined