run_metadata: 41673

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
41673	SRR5119942	SRX2435217	SRS1870213	SRP095327	PRJNA358007	Estrogen sensing by GPER1 activates PI3K/mTOR to promote gender dimorphism in liver growth and cancer	GSE92544	Transcriptome Analysis	Liver cancer is a common cause of cancer death with a male predominant incidence due in part to increased estrogen levels in cirrhotic patients. It is unknown however how estrogen is sensed to influence this process. Here we show that estrogen activates the G protein coupled estrogen receptor 1 GPER1 expressed in hepatocytes to enhancing hepatocyte size cell cycle progression and cell proliferation thereby increasing liver growth in zebrafish larvae and adults. GPER1 stimulation activates PI3K/mTOR signaling and mTOR is essential for both normal and regenerative organ growth. Genetic loss of GPER1 diminishes and estrogen exposure accelerates chemical carcinogenesis specifically in males. Chemical inhibition of GPER1 significantly reduces cancer incidence and progression in a gender specific fashion. Our studies identify GPER1 as a hepatic estrogen sensor that mediates gender dimorphic growth mTOR activation and can serve as a therapeutic target for liver cancer treatment. Overall design: RNA Seq analysis of control DMSO treated livers and ß Estradiol exposed livers were examined.		pubmed:30641053		GC20 WT Male E2 2	GSM2432113		source name:liver β Estradiol\|tissue:liver\|developmental stage:adult\|genotype:Wild type	GC20 WT Male E2 2	Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using cutadapt then mapped to UCSC danRer7 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: danRer7 Supplementary files format and content: excel files include RPKM values for each Sample	liver β Estradiol	Zebrafish were raised until at 3 mpf Fish were then treated daily with DMSO or β Estradiol for a period of 6 weeks.	Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol	All zebrafish was maintained according to the standard Institutional Animal Care and Use Committee guidelines IACUC. At 3 mpf a selected group of wild type male and female zebrafish were seperated into individual tanks to control food consumption.	tissue:liver\|developmental stage:adult\|genotype:Wild type	GSM2432113	GSM2432113: GC20 WT Male E2 2; Danio rerio; RNA Seq	GSM2432113		1	Adult zebrafish livers were surgically isolated and RNA was extracted in Trizol Life Technologies isopropanol precipitated and ethanol washed. RNA was DNase treated using TURBO DNA free kit Life Technologies and RNA quality and quantity were determined using Qubit Thermo Fisher and bioanalyzer Agilent. For library construction NEBNext Directional RNA Library Prep Kit for Illumina #E7420L was used according to the company's protocol	GEO Accession:GSM2432113	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP095327			GC20_WT_Male_2_E2_R1_.final.fastq.gz	fastq	1716932758.0	22757647.0	GSM2432113 r1	0:75.44 1:0	A:438799191;C:399722209;G:404593734;T:473746439;N:71185	75	0			438799191	399722209	404593734	473746439	71185	SRX2435217	SRS1870213	SRA505252	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.96898		0.044		0.86149		0.2305		72		B		usable mapping rate	illumina	nextseq	unknown	random_priming	nebnext	bulk	unknown	unknown		United States	2016-12-19	Adult	Adult	Liver	Liver and Biliary System