run_metadata: 53281

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
53281	SRR9735169	SRX6492129	SRS5140725	SRP216059	PRJNA556239	Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish]	GSE134733	Transcriptome Analysis	Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within minutes and within hours when inhibiting ASC 1 in our in vitro cell models. Our study points to increased ROS generation and reduced mitochondrial respiratory capacity as central early mechanisms in development of visceral adiposity and a role for adipocyte D serine transport via ASC 1 in these processes. Enhancing ASC 1 expression and/or activity in adipocytes likely through primary effects on one carbon metabolism and redox balance is a promising therapeutic strategy for reducing visceral adiposity and related diseases. Overall design: Total RNA Seq of Zebrafish adipose tissue were sequenced on the Illumina HiSeq4000 platform	parent bioproject:PRJNA557596			Adipose WT A1	GSM3964258		source name:Adipose\|genotype:WT\|age:6 month\|tissue:Adipose	Adipose WT A1	Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ...	Adipose	Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day.	Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols	Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank.	genotype:WT\|age:6 month\|tissue:Adipose	GSM3964258	GSM3964258: Adipose WT A1; Danio rerio; RNA Seq	GSM3964258		1	Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM3964258	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000		SRP216059			WT-A1_S49_R1_001.fastq WT-A1_S49_R2_001.fastq	fastq fastq	4250306891.0	28182505.0	GSM3964258 r1	0:75.44 1:75.37	A:1119067057;C:999399803;G:974466658;T:1152728469;N:4644904	75	75			1119067057	999399803	974466658	1152728469	4644904	SRX6492129	SRS5140725	SRA925242	GEO	Hormone Laboratory, Clinical Institute, University of Bergen	2	0.92921	0.93037	0.08377	0.08425	0.63727	0.64122	0.48849	0.49306	75	76	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	unknown	bulk	unknown	unknown		Norway	2019-07-23	Adult	Adult	Adipose Tissue	Adipose Tissue