{"database": "metadata", "table": "run_metadata", "rows": [[29819, "SRR27496349", "SRX23167486", "SRS20117074", "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.", null, "pubmed:38467419", null, "Liver 6dpf DMSO rep2", "GSM8012204", null, "source name:Liver|tissue:Liver|genotype:AB|treatment:DMSO|geo loc name:missing|collection date:missing", "Liver 6dpf DMSO rep2", "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\u2019s 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:DMSO", "GSM8012204", "GSM8012204: Liver 6dpf DMSO rep2; Danio rerio; RNA Seq", "GSM8012204 r1", "GSM8012204", "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP483191", null, "loader:fastq load.py", "DMSO_2_R1.fastq.gz DMSO_2_R2.fastq.gz", "fastq fastq", 3062768334.0, 10141617.0, "GSM8012204 r1", "0:151 1:151", "A:815902447;C:711030547;G:726159250;T:809648102;N:27988", 151, 151, null, null, 815902447, 711030547, 726159250, 809648102, 27988, "SRX23167486", "SRS20117074", "SRA1784007", "Regeneration and Stress Biology, IRIBHM, ULB", "Regeneration and Stress Biology, IRIBHM, ULB", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Belgium", "2024-01-11", "Larval", "Larval", "Liver", "Liver and Biliary System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["29819"], "units": {}, "query_ms": 8.62561899702996}