run_metadata: 41366

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
41366	SRR4369386	SRX2224016	SRS1731677	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 response of the zebrafish digestive organs to an acute high fat feed using RNASeq analysis and highlight the changes in gene expression involved in the synthesis storage and dispersal of lipids. These key physiological responses to a high fat meal all stem from the endoplasmic reticulum ER where lipids are formed and assigned to their 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.		pubmed:27655916		4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3	GSM2339153		source name:digestive organs intestine liver pancreas of 10 zebrafish larvae\|strain:AB\|tissue:intestine liver pancreas\|age:6.5 dpf	4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3	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 time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC. RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base 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	GSM2339153	GSM2339153: 4h high fat fed 6.5 dpf zebrafish larvae high fat cohort rep3; Danio rerio; RNA Seq	GSM2339153		1	At the appropriate time points digestive organs intestine liver pancreas were dissected from 10 anesthetized larval zebrafish and immediately transferred into 30 uL RNALater Ambion. The samples were stored at 20oC thawed on ice and RNA was extracted using an RNAqueous Micro Kit Ambion and stored at 80oC. RNA sample purity was verified with the Agilent RNA 6000 Pico Kit and an Agilent 2100 Bioanalyzer Agilent Technologies. cDNA libraries were constructed from polyA selected RNA using the Illumina TruSeq RNA Sample Prep Kit v2 Illumina following the LS low sample throughput option. Six samples were run per lane on an Illumina HiSeq2000 for a 50 base pair plus indexing run.	GEO Accession:GSM2339153	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP090938			EZ143.fq.gz	fastq	3620501750.0	72410035.0	GSM2339153 r1	0:50	A:928100369;C:870292711;G:888545580;T:933466612;N:96478	50				928100369	870292711	888545580	933466612	96478	SRX2224016	SRS1731677	SRA482638	GEO	Yixian Zheng, Embryology, Carnegie Institution for Science	1	0.93833		0.05511		0.75032		0.55771		50		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown		United States	2016-10-06	Larval	Larval	Multi-tissue	Multi-system