{"database": "metadata", "table": "run_metadata", "rows": [[41078, "SRR3655795", "SRX1836009", "SRS1495472", "SRP076398", "PRJNA325275", "Short Bowel Syndrome SBS has Widespread Effects Beyond Altering Nutrient Absorption:  RNA Sequencing a Zebrafish SBS Model", "GSE83195", "Transcriptome Analysis", "Purpose: Most of the morbidity associated with short bowel syndrome SBS are attributed to effects of decreased enteral nutrition and administration of total parenteral nutrition TPN. We hypothesized that acute SBS alone has significant systemic effects  and tested this in a zebrafish SBS model. Methods: With IACUC approval  adult male wild type zebrafish underwent SBS laparotomy  proximal stoma  distal ligation n=3 or sham laparotomy alone n=3 surgery. post 2 weeks  the proximal intestine was harvested  RNA isolated and external RNA controls consortium ERCC controls spiked into each sample  sequenced and aligned to reference genome with gene ontology GO enrichment analysis performed.  CyclinD1  CyclinB1  SAA1  IFN gamma  and CYP7A1 gene expression were confirmed by qPCR. Results: RNA seq analysis identified 1346 up regulated genes and 678 down regulated genes in SBS zebrafish compared to sham. The up regulated genes were involved in acute phase response signaling  complement system  coagulation  cell proliferation  cellular barrier  production of nitric oxide & reactive oxygen species and bile acid biosynthesis. The down regulated genes were involved in folate synthesis  gluconeogenesis  glycogenolysis  fatty acid oxidation & activation  and drug & steroid metabolism. CyclinD1 gene expression was 2 fold higher  CyclinB1 2.8 fold higher  SAA1 4.5 fold higher  IFN gamma 2.1 fold higher  and CYP7A1 25 fold higher in SBS than sham by qPCR. Conclusion: The gene expression of SBS demonstrates complex and extensive alteration of multiple pathways  some previously implicated as effects of TPN. The systemic complications of SBS alone are significant and extend beyond the complications of therapy. Overall design: Profiles of paired fed and unfed zebrafish  intestine were generated by deep sequencing in triplicate.", null, "pubmed:28118819", null, "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "GSM2195932", null, "tissue:full thickness intestine|status:SHAM", "Proximal S1 intestine in zebrafish 2 wks post sham surgery #3", "Sequencing QC: FastQC Trimming of reads for quality: Trimmomatic Alignment: STAR Read binning: Htseq count Differential Gene Expression: RUVSeq  edgeR Genome build: UCSC GRCz10/danRer10 Supplementary files format and content: Tab delimited text file with RPKM values  counts  DE statistics and Annotation Supplementary files format and content: BigWig Files for UCSC Genome Browser", "full thickness intestine", null, "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", null, "status:SHAM", "GSM2195932", "GSM2195932: Proximal S1 intestine in zebrafish 2 wks post sham surgery #3; Danio rerio; RNA Seq", "GSM2195932", null, "1", "Full thickness section of intestine was removed  and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer. Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations", "GEO Accession:GSM2195932", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP076398", null, null, "02May15_KS383.fastq.gz", "fastq", 1510741670.0, 20138480.0, "GSM2195932 r1", "0:75.02 1:0", "A:374411447;C:361418430;G:359803924;T:415021333;N:86536", 75, 0, null, null, 374411447, 361418430, 359803924, 415021333, 86536, "SRX1836009", "SRS1495472", "SRA432774", "GEO", "Children's Hospital Los Angeles", 1, 0.94789, null, 0.05269, null, 0.77753, null, 0.53939, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-09", "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": ["41078"], "units": {}, "query_ms": 11.519689999659022}