run_metadata: 44999
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 |
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| 44999 | SRR6411468 | SRX3504483 | SRS2782037 | SRP127389 | PRJNA427282 | RNA profiling of the liver and gut tissues in zebrafish Danio rerio [miRNA] | GSE108436 | 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 miRNome in adult zebrafish tissues gut and liver under homesostasis. | parent bioproject:PRJNA427275 | pubmed:30386173 | Gut 4 miRNA | GSM2898188 | source name:Gut|tissue:Gut|Sex:male | Gut 4 miRNA | 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. Gut 1 Gut 2 Liver 1 and Liver 2 contain raw count data for the two gut and liver miRNAseq libraries respectively. Symbol GeneID Description and MirBaseID represent miRNA annotation and description information. | Gut | 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 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 | tissue:Gut|Sex:male | GSM2898188 | GSM2898188: Gut 4 miRNA; Danio rerio; miRNA Seq | GSM2898188 | 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:GSM2898188 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP127389 | 4.fastq.gz | fastq | 643103727.0 | 12609877.0 | GSM2898188 r1 | 0:51 | A:158299708;C:154230134;G:180978224;T:147874496;N:1721165 | 51 | 158299708 | 154230134 | 180978224 | 147874496 | 1721165 | SRX3504483 | SRS2782037 | SRA641250 | GEO | Walton RS311, Pathology, Medical University of South Carolina | 1 | 0.0075 | 0.00106 | 0.99671 | 0.56044 | 51 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | trueseq | bulk | unknown | unknown | United States | 2017-12-22 | Undetermined | Adult | Gut | Digestive System |