{"database": "metadata", "table": "run_metadata", "rows": [[41376, "SRR4369376", "SRX2224006", "SRS1731668", "SRP090938", "PRJNA345605", "Transcriptional responses in 6.5 dpf larval zebrafish guts upon feeding a high fat or low fat meal", "GSE87704", "Transcriptome Analysis", "We report the transcriptional\u00a0response\u00a0of the zebrafish digestive organs\u00a0to an acute high fat feed using\u00a0RNASeq\u00a0analysis\u00a0and highlight the changes in gene\u00a0expression\u00a0involved in the synthesis  storage  and dispersal of lipids.\u00a0These key physiological responses to a high fat meal all\u00a0stem from\u00a0the endoplasmic reticulum ER  where lipids are formed and assigned\u00a0to\u00a0their fates. Overall design: A feeding time course was undertaken with 6.5 dpf larval zebrafish. Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. At the appropriate time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish. Unfed controls were used to determine a transcriptional baseline.", null, "pubmed:27655916", null, "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "GSM2339143", null, "source name:digestive organs intestine  liver  pancreas of 10 zebrafish larvae|strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1", "Reads were mapped to the zebrafish genome Zv9 by Tophat2. Refseq annotation was used as known GTF. bedgrah files for visualization were generated by custom scripts. reads falling on genes were counted by custom scripts and differentially expressed genes were called by edgeR. Genome build: Zv9 Supplementary files format and content: bedgraph files for read densities along the genome RPKM were generated using custom scripts.", "digestive organs intestine  liver  pancreas of 10 zebrafish larvae", "Triplicate samples were independently prepared from pairwise crosses fed either high fat or low fat food. 5% egg yolk emulsion high fat feeds and 10% egg white low fat feeds were prepared. For all feeding solutions  a total volume of 20 mL was prepared.", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "For all experiments  WT AB background embryos were collected from natural spawning  staged  and raised in zebrafish embryo media EM", "strain:AB|tissue:intestine  liver  pancreas|age:6.5 dpf", "GSM2339143", "GSM2339143: 1h low fat fed 6.5 dpf zebrafish larvae low fat cohort rep1; Danio rerio; RNA Seq", "GSM2339143", null, "1", "At the appropriate\u00a0time points  digestive organs intestine  liver  pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30\u00a0uL\u00a0RNALater\u00a0Ambion. The samples were stored at  20oC  thawed on ice  and RNA was extracted using an\u00a0RNAqueous\u00a0Micro Kit Ambion and stored at  80oC.\u00a0 RNA sample purity was verified with\u00a0the Agilent RNA 6000 Pico Kit\u00a0and\u00a0an\u00a0Agilent 2100\u00a0Bioanalyzer\u00a0Agilent Technologies.\u00a0cDNA\u00a0libraries were constructed from polyA selected RNA using the\u00a0Illumina\u00a0TruSeq\u00a0RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an\u00a0Illumina\u00a0HiSeq2000 for a 50\u00a0base pair plus indexing run.", "GEO Accession:GSM2339143", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090938", null, null, "EZ211.fq.gz", "fastq", 2627126000.0, 52542520.0, "GSM2339143 r1", "0:50", "A:679161674;C:624785100;G:633592207;T:689524385;N:62634", 50, null, null, null, 679161674, 624785100, 633592207, 689524385, 62634, "SRX2224006", "SRS1731668", "SRA482638", "GEO", "Yixian Zheng, Embryology, Carnegie Institution for Science", 1, 0.93885, null, 0.06121, null, 0.74629, null, 0.53653, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "Larval", "Larval", "Multi-tissue", "Multi-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": ["41376"], "units": {}, "query_ms": 10.090616000525188}