run_metadata: 71957

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
71957	SRR22143711	SRX18123007	SRS15624881	SRP405931	PRJNA896973	Vitamin D Receptor regulation of hepatic energy metabolism in zebrafish	GSE217120	Transcriptome Analysis	Vitamin D deficiency and mutations in Vitamin D Receptor VDR are associated with liver disease and obesity but the functions of vitamin D signaling in metabolism are poorly understood. Though vitamin D signaling is best known for its functions in mineral homeostasis and skeleton calcification in terrestrial vertebrates this is unlikely to be the evolutionary function of vitamin D signaling. We utilize tissue specific genetic modulation of Vdr signaling to investigate the function of the vitamin D endocrine system in zebrafish. We find that hepatocyte Vdr regulates organismal response to nutritional cues and coordinates hepatic and organismal energy metabolism by balancing energy storage and tissue growth. Overall design: Comparative gene expression profiling analysis of RNA seq data following hepatocyte specific Vdr modulation in larval and adult zebrafish. fabp10a:dn vdra and fabp10a:ca vdra transgenes were used to achieve hepatocyte Vdr impairment or hyperactivation respectively. Larval experiments were performed on sorted hepatocytes at 96 hpf and reflect approximately 35 pooled fish per sample. Adult experiments were performed on dissected male liver collected at 4.5 mpf mpf and are composed of 3 livers per sample. wild type controls are included for each experiment. For larval fabp10a:dn vdra N = 4 wt 4 dn vdra. For fabp10a:ca vdra N = 4 wt 3 ca vdra. For adult fabp10a:dn vdra N = 4 wt 4 dn vdra.		pubmed:38944835		hepatocytes 96hpf cavdra expt2 rep3	GSM6705365		tissue:hepatocytes sorted\|cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	hepatocytes 96hpf cavdra expt2 rep3	FASTQ files were mapped to GRCz11 using STAR v2.5.3 and read counting was performed using HTSeq v0.11.1. Read count normalization was performed using the R package DEseq2. Assembly: GRCz11 Supplementary files format and content: .csv files containing ensembl ids gene names and raw read counts or normalized read counts for each experiment	hepatocytes sorted		Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.	Larval zebrafish were reared at 28.5 C in E3 salt solution. Adult fish were reared in density matched tanks and fed artemia twice daily.	cell type:hepatocytes sorted\|genotype:fabp10a:ca vdra\|time:96 hpf	GSM6705365	GSM6705365: hepatocytes 96hpf cavdra expt2 rep3; Danio rerio; RNA Seq	GSM6705365 r1	GSM6705365	1	Hepatocytes were sorted into 75 uL Buffer RLT containing b mercaptoethanol. Total RNA was extracted using the Qiagen RNA Micro Kit with on column DNase treatment. cDNA synthesis and amplification were performed according to the Smart seq2 protocol https://doi.org/10.1038/nprot.2014.006. Library prep was performed with the Nextera XT DNA Library Preparation Kit Illumina.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP405931			cavdra_expt2_rep3_R1.fastq.gz	fastq	6706002750.0	44706685.0	GSM6705365 r1	0:150 1:0	A:1750156238;C:1597023915;G:1614921548;T:1743765130;N:135919	150	0			1750156238	1597023915	1614921548	1743765130	135919	SRX18123007	SRS15624881			Goessling Lab, Brigham and Women's Hospital	1	0.88313		0.04409		0.87661		0.55505		150		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	nextera	sc	single_cell_plate	smartseq		United States	2022-11-02	Multi-stage	Multi-stage	Liver	Liver and Biliary System