run_metadata: 45005

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
45005	SRR6411470	SRX3504485	SRS2782039	SRP127390	PRJNA427283	RNA profiling of the liver and gut tissues in zebrafish Danio rerio [mRNA]	GSE108435	Transcriptome Analysis	Compared to other fish models miRNAs are currently most extensively studied and identified in zebrafish. Approximately 415 dre miRNAs have been identified and several articles have studied some aspect of miRNA function in zebrafish such as their role in basic development and in disease pathways. However this field of research is in its infancy and the function of several dre miRNAs as well as their tissue specific expression profile are yet to be defined. In this study the liver and gut were dissected wildtype/untreated fish total and small RNA were extracted mRNA and miRNA libraries constructed and subjected to high throughput sequencing HTS using standard approaches. We carried out differential expression DE analysis and compared liver miRNA expression to gut using established bioinformatics pipelines. Through bioinformatics analysis known and putative novel miRNAs were identified. Finally we constructed a “miRNA matrix” that connects both total RNA Seq and miRNA Seq. Overall design: Examination of transcriptome in an in vivo model organism in two defined tissues liver and gut.	parent bioproject:PRJNA427275	pubmed:30386173		Liver 2 mRNA	GSM2898182		source name:Liver\|Sex:male\|tissue:Liver	Liver 2 mRNA	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 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 the gut vs liver Comparison. Columns to the right of the Base Mean column represent standard DEseq2 output. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and two liver RNAseq libraries respectively. The ensembl gene id external gene name description represent zebrafish gene identifiers. The human homologs as determined by Ensembl homology are described using the following human gene identifiers hsapiens homolog ensembl gene hgnc symbol Human description and Human entrez geneid	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 . 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 extracting the tissues i.e. liver and intestine. Tissue samples were 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 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.		Sex:male\|tissue:Liver	GSM2898182	GSM2898182: Liver 2 mRNA; Danio rerio; RNA Seq	GSM2898182		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:GSM2898182	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP127390			Liver_2.fastq.gz	fastq	2174570997.0	42638647.0	GSM2898182 r1	0:51	A:548366346;C:555137400;G:541707378;T:528997203;N:362670	51				548366346	555137400	541707378	528997203	362670	SRX3504485	SRS2782039	SRA641251	GEO	Walton RS311, Pathology, Medical University of South Carolina	1	0.91804		0.03093		0.88493		0.59674		51		B		usable mapping rate	illumina	hiseq_era	unknown	small_rna	trueseq	bulk	unknown	unknown		United States	2017-12-22	Undetermined	Undetermined	Liver	Liver and Biliary System