run_metadata: 42540

This data as json

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42540	SRR5742108	SRX2947055	SRS2306351	SRP110158	PRJNA391470	SYSTEMS ANALYSIS OF THE LIVER TRANSCRIPTOME IN ADULT MALE ZEBRAFISH EXPOSED TO THE NON IONIC SURFACTANT NONYLPHENOL NP.	GSE100369	Transcriptome Analysis	We report the effects of exposure to the endocrine disruptor nonylphenol NP on transcriptome modification in the livers of in vivo Zebrafish. Our data indicate changes in fatty acid metabolism and inflammation pathways associated with the development of Non Alcoholic Fatty Liver Disease NAFLD. Overall design: Examination of transcriptome changes in an in vivo model organism exposed to a common environmental compound.		pubmed:30563618		CL61	GSM2679635		tissue:Liver\|agent:100 nM Nonylphenol NP\|Sex:male	CL61	Sequencing was carried out on an Illumina GAIIx. 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 resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene level differential expression analyses. Transcript count data from DESeq2 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 DESEQ2 output for each Comparison with gene identifier information. We exploited Ensembl homology to append a human entrez gene ID to a given zebrafish entrez gene ID. The headings in the file related to the zebrafish transcript and its human ortholog are as follows; ensembl gene id; external gene name; description; hsapiens homolog ensembl gene; hgnc symbol; Human description; Human entrez geneid; ensembl peptide ids; ensembl transcript ids. The baseMean log2FoldChange lfcSE stat pvalue padj are all derived from DESeq2	Liver	Male zebrafish Danio rerio were housed in aquaria maintained at a temperature 26 29ºC with a 100 W aquarium heater and had a light dark cycle of 14:10 hours. The pH ranged from 7.0 to 7.6 throughout the duration of the experiment. Aeration and filtration were accomplished using sponge filters. Zebrafish were fed twice a day with commercial flaked fish food Tetra Germany. The fish were acclimated one week before the beginning of the experiments. For both experiments 80 L tanks were prepared for each of the experimental groups housing 40 fish per tank. One tank contained water with 1000 nM of 17β estradiol E2 one tank contained 100 nM of nonylphenol NP and one tank contained water with EtOH as a negative control. All chemicals were dissolved in EtOH and stock working solutions were prepared from which the working experimental concentrations were prepared. All exposures utilized a continuous flow through system and all exposures lasted for three weeks. post the end of the experimental period the zebrafish were anaesthetized using 3 aminobenzoic acid ethyl ester Sigma Aldritch St. Louis MO; 10 g/L tap water and sacrificed for removal of their livers which were immediately frozen in liquid nitrogen and stored at 70ºC for molecular biology analysis.	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.		agent:100 nM Nonylphenol NP\|Sex:Male	GSM2679635	GSM2679635: CL61; Danio rerio; RNA Seq	GSM2679635		1	Isolation of total liver RNA was performed using TRIzol reagent Invitrogen and the extracted RNA were further purified using the RNeasy Mini kit Qiagen Valencia California. All RNA were treated with DNase to ensure no DNA appeared in the results. To prepare RNA Seq libraries using the TruSeq RNA Sample Prep Kit Illumina San Diego CA 100 200 ng of total RNA was used following the protocol described by the manufacturer.	GEO Accession:GSM2679635	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina Genome Analyzer IIx		SRP110158			M-CL61.fa.fastq.gz	fastq	127229214.0	3029267.0	GSM2679635 r1	0:42	A:32179832;C:24929970;G:35004390;T:35109199;N:5823	42				32179832	24929970	35004390	35109199	5823	SRX2947055	SRS2306351	SRA579535	GEO	Walton RS311, Pathology, Medical University of South Carolina															illumina	early_illumina	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2017-06-22	Undetermined	Undetermined	Liver	Liver and Biliary System