run_metadata: 41074

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
41074	SRR3655799	SRX1836011	SRS1495475	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.		pubmed:28118819		Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2	GSM2195934		tissue:full thickness intestine\|status:SBS	Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2	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		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		status:SBS	GSM2195934	GSM2195934: Proximal S1 intestine in zebrafish 2 weeks post SBS surgery #2; Danio rerio; RNA Seq	GSM2195934		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:GSM2195934	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP076398			02May15_KS409.fastq.gz	fastq	1422635421.0	18963577.0	GSM2195934 r1	0:75.02 1:0	A:362173330;C:332883466;G:329078937;T:398420070;N:79618	75	0			362173330	332883466	329078937	398420070	79618	SRX1836011	SRS1495475	SRA432774	GEO	Children's Hospital Los Angeles	1	0.92474		0.07466		0.73423		0.50871		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2016-06-09	Larval	Larval	Gut	Digestive System