{"database": "metadata", "table": "run_metadata", "rows": [[45004, "SRR6411471", "SRX3504486", "SRS2782040", "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 \u201cmiRNA matrix\u201d 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", null, "Gut 3 mRNA", "GSM2898183", null, "source name:Gut|Sex:male|tissue:Gut", "Gut 3 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\u2019s 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", "Gut", "Male zebrafish were housed in aquaria that were individually heated using a 100 W aquarium heater to maintain a temperature of 26\u201329 \u00b0C  and the light\u2013dark 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 \u201370 \u00b0C. 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.", null, "Sex:male|tissue:Gut", "GSM2898183", "GSM2898183: Gut 3 mRNA; Danio rerio; RNA Seq", "GSM2898183", null, "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:GSM2898183", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP127390", null, null, "Gut_1.fastq.gz", "fastq", 2336820153.0, 45820003.0, "GSM2898183 r1", "0:51", "A:592745033;C:551283776;G:583859269;T:608544280;N:387795", 51, null, null, null, 592745033, 551283776, 583859269, 608544280, 387795, "SRX3504486", "SRS2782040", "SRA641251", "GEO", "Walton RS311, Pathology, Medical University of South Carolina", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-12-22", "Undetermined", "Undetermined", "Gut", "Digestive System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["45004"], "units": {}, "query_ms": 12.383338000290678}