run_metadata: 43052

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
43052	SRR5883563	SRX3049652	SRS2396334	SRP114397	PRJNA396509	The plasticizer Bisphenol A favors cancer progression in adult zebrafish by perturbing the epigenome: A systems level analysis of the miRNome miRNA.	GSE102059	Transcriptome Analysis	Exposure to bisphenol A BPA an endocrine disruptor ED has raised concerns for both human and ecosystem health. Epigenetic factors including microRNAs are key regulators of gene expression during cancer. The effect of BPA exposure on the zebrafish epigenome remains poorly characterized. Zebrafish represents an excellent model to study cancer as the organism develops disease that resembles human cancer. Using zebrafish as systems toxicology model we hypothesized that chronic BPA exposure impacts the miRNome in adult zebrafish and establishes an epigenome more susceptible to cancer development. post a 3 week exposure to 100 nM BPA RNA from the liver was extracted to perform high throughput mRNA and miRNA sequencing. Differential expression DE analyses comparing BPA exposed to control specimens were performed using established bioinformatics pipelines. In the BPA exposed liver 6 188 mRNAs and 15 miRNAs were differently expressed q = 0.1. By analyzing human orthologs of the DE zebrafish genes signatures associated with non alcoholic fatty liver disease NAFLD oxidative phosphorylation mitochondrial dysfunction and cell cycle were uncovered. Chronic exposure to BPA has a significant impact on the liver miRNome in adult zebrafish and has the potential to cause adverse outcomes including cancer. Overall design: Examination of miRNome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:29027980		Liver CNTRL 4 5	GSM2722575		tissue:Liver\|exposure:Control	Liver CNTRL 4 5	Sequencing was carried out on an Illumina HiSeq2000. Illumina Casava1.8 software used for basecalling. Sequenced reads fastq files were trimmed for adaptor sequence and masked for low complexity or low quality sequence Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform OnRamp Bioinformatics San Diego CA. OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data including data validation and quality control and read alignment to the ZEBRAFISH genome GRCZ10 using tophat2 The Comprehensive Analysis Pipeline for microRNA sequencing data CAP miRSeq was used for read pre processing alignment mature/precursor/ novel miRNA detection and quantification and data visualization. The miRNA Seq data was aligned to GRCz10 zebrafish genome using miRDeep a tool for miRNA identification from RNA sequencing data and Bowtie. DE analysis was performed with EdgeR. Transcript count data from EdgeR analysis of the samples were sorted according to their adjusted p value or q value which is the smallest false discovery rate FDR at which a transcript is called significant. Genome build: GRCz10 Supplementary files format and content: tab delimited .txt files include the EdgeR output for the BPA vs Control Comparison. Columns to the right of the logFC column represent EdgeR output. CNTRL 1.3 CNTRL 4.5 Liver BPA 1.3 Liver BPA 4.5 contain raw count data for the two control and two BPA exposed liver miRNAseq libraries. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information.	Liver	Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26–29 °C and the light–dark cycle was 14:10 h. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were provided using sponge filters. Fish were fed two times a day with commercial flaked fish food Tetra Germany. Fish were acclimated for one week prior to commencing the experiments. Four tanks 80 l/tank with 20 animals each were prepared for the different experimental groups two containing water with 100 nM BPA and two containing only water as negative control. BPA was dissolved in ethanol and a stock working solutions was prepared from which the working experimental concentrations were prepared. The nominal exposures utilized a continuous flow through system. Following a three week exposure the fish were sampled for liver; tissue samples were then immediately frozen in liquid nitrogen and stored at –70 °C. All the animals were treated humanely and with regard for alleviation of suffering. These procedures followed an approved institutional IACUC protocol.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA		exposure:Control	GSM2722575	GSM2722575: Liver CNTRL 4 5; Danio rerio; miRNA Seq	GSM2722575		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the miRNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. The miRNA Seq libraries were prepared using with Illumina TruSeq Small RNA Prep kit and 1 ug input RNA	GEO Accession:GSM2722575	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP114397			10_CGTACG_LALL_R1_001.fastq.gz	fastq	407289621.0	7986071.0	GSM2722575 r1	0:51	A:84982391;C:104532595;G:122785928;T:93918201;N:1070506	51				84982391	104532595	122785928	93918201	1070506	SRX3049652	SRS2396334	SRA594837	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.13902		0.01445		0.99086		0.57915		51		B		usable mapping rate	illumina	hiseq_era	unknown	size_fractionation	trueseq	bulk	unknown	unknown		United States	2017-07-31	Undetermined	Adult	Liver	Liver and Biliary System