run_metadata: 29818

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
29818	SRR27496348	SRX23167487	SRS20117075	SRP483191	PRJNA1063616	Protection from starvation induced liver atrophy.	GSE252997	Transcriptome Analysis	Starvation causes the accumulation of lipid droplets in the liver a somewhat counterintuitive phenomenon that is nevertheless conserved from flies to humans. Much like fatty liver resulting from overfeeding hepatic lipid accumulation steatosis during undernourishment can lead to lipotoxicity and atrophy of the liver. Here we found that while surface populations of Astyanax mexicanus undergo this evolutionarily conserved response to starvation the starvation resistant cavefish larvae of the same species do not display an accumulation of lipid droplets upon starvation. Moreover cavefish are resistant to liver atrophy during starvation providing a unique system to explore strategies for liver protection. Using comparative transcriptomics between zebrafish surface fish and cavefish we identified the fatty acid transporter slc27a2a/fatp2 to be correlated with the development of fatty liver. Pharmacological inhibition of slc27a2a in zebrafish rescues steatosis and atrophy of the liver upon starvation. Further down regulation of FATP2 in drosophila larvae inhibits the development of starvation induced steatosis suggesting the evolutionary conserved importance of the gene in regulating fatty liver upon nutrition deprivation. Overall our study identifies a conserved druggable target to protect the liver from atrophy during starvation. Overall design: Zebrafish larvae at 4 dpf were treated with Lipofermata 5 uM or vehicle DMSO for 48 hours. During treatment no exogenous food was added. At 6 dpf the livers were isolated for RNA Sequencing. Experiment was performed in duplicate.		pubmed:38467419		Liver 6dpf Lipofermata rep1	GSM8012205		source name:Liver\|tissue:Liver\|genotype:AB\|treatment:Lipofermata\|geo loc name:missing\|collection date:missing	Liver 6dpf Lipofermata rep1	Raw reads were mapped using HiSAT2 against the GRCz11 zebrafish genome and counted using FeatureCounts. For normalization differential gene expression analysis and GO analysis iDEP version 0.951 was utilized with default parameters. For differential gene expression a fold change of 2 and false discovery rate of 0.1 was used for cut off. Assembly: GRCz11 Supplementary files format and content: comma separate file csv with raw counts for all samples.	Liver	Lipofermata or DMSO treatment for 48 hours	For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture’s instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.	Zebrafish larvae at 6 dpf.	tissue:Liver\|genotype:AB\|treatment:Lipofermata	GSM8012205	GSM8012205: Liver 6dpf Lipofermata rep1; Danio rerio; RNA Seq	GSM8012205 r1	GSM8012205	1	For RNA Seq mRNA was isolated from livers at 6 dpf. For this livers from 30 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems Promega Z6110. mRNA was isolated from the lysed tissue by following the manufacture's instruction. cDNA synthesis library preparation and Illumina sequencing was performed by Eurofins Genomics Europe Sequencing GmbH. Integrity and quantity of the starting mRNA was determined by appropriate methods e.g. measurement of volume and quantity gel electrophoresis and/or fluorimeter measurements. Library preparation incorporated adaptor sequence adapters and indexing compatible for Illumina sequencing technology using proprietary methods of Eurofins Genomics Europe Sequencing GmbH. The protocol for RNA library preparation was based on NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. For cDNA library preparation post first strand synthesis the second strand synthesis was performed using dUPT. The ends of the double stranded cDNA fragments were repaired and dATP ligated to the blunt ended fragments. Next the sequencing adapters were ligated to the DNA fragments and the dUTP containing second strand was removed. Sequencing was performed on the Illumina NovaSeq 6000 platform using 2x150 Sequence mode.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP483191		loader:fastq load.py	Lipofermata_1_R1.fastq.gz Lipofermata_1_R2.fastq.gz	fastq fastq	3645146040.0	12070020.0	GSM8012205 r1	0:151 1:151	A:981366033;C:836975744;G:858564002;T:968208667;N:31594	151	151			981366033	836975744	858564002	968208667	31594	SRX23167487	SRS20117075	SRA1784007	Regeneration and Stress Biology, IRIBHM, ULB	Regeneration and Stress Biology, IRIBHM, ULB												B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	unknown	unknown		Belgium	2024-01-11	Larval	Larval	Liver	Liver and Biliary System