run_metadata: 55499

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
55499	SRR10511892	SRX7200006	SRS5705561	SRP231178	PRJNA591019	Gene expression in the adult zebrafish intestine during starvation and refeeding	GSE140821	Transcriptome Analysis	In this RNA Seq dataset we describe transcriptomic changes in whole dissected intestinal tracts taken from adult zebrafish that were either fed normally or subjected to a prolonged starvation/refeeding regimen. Analysis of this RNA Seq data revealed starvation induced alterations in transcript levels for many genes including a decrease in lipid metabolism and an increase in innate immune responses. Refeeding for as little as 3 days post starvation was sufficient to restore most transcripts to their baseline pre starvation levels. These host RNA Seq results are accompanied by a 16S rRNA gene sequencing dataset from similarly treated adult zebrafish to define changes in intestinal microbiome composition associated with starvation and refeeding. Overall design: This study consists of two treatment groups of adult zebrafish 81dpf dpf that were separately housed. One treatment group control was continuously fed throughout the study while the experimental group was starved for up to 21 days and then refed. At each timepoint 3dpS = 3 days post starvation; 21dpS = 21 days post starvation; 3dpR = 3 days post refeeding 4 zebrafish were taken from each treatment group euthanized and dissected to remove the whole intestine for RNA extraction and RNA Seq analysis.		pubmed:35317738		3dpRFed2Gut3	GSM4187018		source name:Intestine\|tissue:Intestine\|treatment:Continuously fed\|tank:Fed tank 2	3dpRFed2Gut3	Basecalls were performed using CASAVA v1.8 Illumina. Fastq files were trimmed for adapter sequences using Trim galore in Galaxy www.usegalaxy.org version 0.4.3.1. Trimmed fastq files were aligned to the zebrafish genome using STAR in Galaxy version 1.1.6 to yield sorted BAM files. Aligned reads in BAM files were counted using htseq count in Galaxy version 0.9.1 to generate counts files. Coverage bigWig files were generated from sorted BAM files using bamCoverage in Galaxy version 2.5.0.0 for visualization in the UCSC Genome Browser. Counts files generated via htseq count were used to estimate log2 fold changes in gene expression via Deseq2 Version 3.10 in R Version 3.6. Genome build: zv10	Intestine		Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer’s instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.	All zebrafish experiments were conducted in conformity with the Public Health Service Policy on Humane Care and Use of Laboratory Animals using protocols approved by the Institutional Animal Care and Use Committee of Duke University. Unless otherwise stated all fish were maintained on a 14 hour light cycle at 28 degrees Celsius. All zebrafish used for were born on the same day from 1 breeding pair from a single sibship. Fertilized embryos were transferred into Petri dishes containing egg water 6g sea salt 1.5g calcium sulfate 0.75g sodium bicarbonate 10 12 drops methylene blue 10L water at a density of 50 embryos/dish at incubated at 28.5 degrees Celsius. At 1 dpf dpf embryos were transferred to 3L tanks containing 500mL water from a recirculating zebrafish aquaculture system system water. Each tank contained 30 embryos. Fish were then maintained under standard zebrafish husbandry until the start of the experiment at 60dpf. Zebrafish were then randomly transferred into four clean 10L tanks at a density of 44 fish per tank with half the tanks receiving no food for the following 21 days. Following the 21 days of starvation feedings for all tanks were allowed to occur as per standard husbandry: two feedings of Artemia per day interspersed with two feedings of Gemma 300 Skretting. Over the 21 days of starvation and 21 days of refeeding we observed no mortality.	tissue:Intestine\|treatment:Continuously fed\|tank:Fed tank 2\|age dpf = dpf	GSM4187018	GSM4187018: 3dpRFed2Gut3; Danio rerio; RNA Seq	GSM4187018		1	Frozen intestinal samples stored in Trizol at 80oC were homogenized using Zirconium oxide beads Biospec 11079107 and a Vortex Genie2 Scientific Industries 1311 V fitted with a Vortex Adapter Scientific Industries 13000 V1 24 in three 45 second intervals. Samples were put on ice in between homogenization to prevent overheating. Following homogenization a phase separation was performed by adding 200ul of chloroform to each sample and mixing by vigorous inversion 15 times. Samples were then incubated at room temperature for 3 minutes and centrifuged at 12000rcf for 15min at 4oC. 500ul of the aqueous upper phase from each sample was then transferred to a new Eppendorf tube to which 500uL 70% Ethanol in DEPC water was added and vortexed. Following phase separation samples were DNase treated and total RNA was extracted via column purification using the PureLink DNase Set Thermo Fisher 12185010 and the PureLink RNA Mini kit Thermo Fisher 12183025 according to the manufacturer's instructions. Final sample quality and concentration were assessed via spectrophotometry and samples were stored at 80oC until submission to the Duke Sequencing and Genomic Technologies Core. RNA seq libraries were prepared and sequenced by Duke Sequencing and Genomic Technologies Core on an Illumina HiSeq 2500 50bp single end read according to the manufacturer's instructions. Prior to library preparation RNA was extracted using the Ribozero Gold Kit Cat #20020598 according to the manufacturer's instructions.	GEO Accession:GSM4187018	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP231178			SC_20_concat_R1.fastq.gz	fastq	1429183557.0	28023207.0	GSM4187018 r1	0:51 1:0	A:406259184;C:299540462;G:297537630;T:425792267;N:54014	51	0			406259184	299540462	297537630	425792267	54014	SRX7200006	SRS5705561	SRA1000332	GEO	Molecular Genetics and Microbiology, Duke University	1	0.93776		0.10446		0.75659		0.51357		51		B		usable mapping rate	illumina	hiseq_era	unknown	rrna_depletion	ribozero	bulk	unknown	unknown		United States	2019-11-21	Multi-stage	Multi-stage	Gut	Digestive System