biostudies-arrayexpressDaniel GorskiMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-12700We generated a tamoxifen-inducible, adipocyte-specific ATGL-KO animals to analyze the role of adipocyte ATGL in cardiac ischemia/reperfusion. KO was induced in 10 weeks old male mice via 7d of consecutive i.p.-injections of 500µg hydroxytamoxifen/day. Pnpla2-flox homozygous, Cre-negative littermates were used as control. After 2 weeks washout phase mice underwent closed chest ischemia with first ligature-induction surgery and 3-7 d later 1 hour closed chest ischemia followed by 24 h reperfusion. Mice were sacrificed and hearts excised to perform spatial transcriptomic analysis on 10X Visium Gene Expression slides. The goal was to identify differences in gene expression between KO and control in the different zones of the heart after ischemia (eg. ischemic, border and remote zone).biostudies-arrayexpressNucleic Acid Extraction - Prepared Visium slides were used as input for the Visium Spatial Gene Expression workflow (10X Genomics, Pleasanton, USA) according to the manufacturer’s instructions. Tissue permeabilization was carried out for 12 minutesSample Collection - After mouse sacrifice hearts were excised and retrograde perfused with first 5ml Heparin/PBS solution followed by 1ml PBS. Perfused hearts were place in OCT, snap-frozen in pre-cooled isopentane (-30 to -40°C) and stored at -80°C until further use. 10µm thick tissue sections were cut in a cryostat at -20°C chamber temperature and -10°C object head temperature and placed at the 10X Visium Gene Expression slide.Sequencing - Sequencing was performed on a NextSeq 2000 system (Illumina Inc. San Diego, USA) with a mean sequencing depth of ~40,000 reads/spot.Library Construction - Library construction was performed to manufacturer’s instructions, the Visium Spatial Gene Expression workflow (10X Genomics, Pleasanton, USA).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - To generate the processed data file in this repository, raw sequencing data were processed using the 10X Genomics spaceranger software (v1.3.1). Aligning reads to the mm10 genome, UMI counting, tissue detection, and fiducial detection were performed via the spaceranger count pipeline.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000spatial transcriptomics by high-throughput sequencingMus musculusDaniel GorskiKatharina BottermannfalseSpatial transcriptomics of adipocyte-specific ATGL-KO mice 24 h after cardiac ischemiaWe generated a tamoxifen-inducible, adipocyte-specific ATGL-KO animals to analyze the role of adipocyte ATGL in cardiac ischemia/reperfusion. KO was induced in 10 weeks old male mice via 7d of consecutive i.p.-injections of 500µg hydroxytamoxifen/day. Pnpla2-flox homozygous, Cre-negative littermates were used as control. After 2 weeks washout phase mice underwent closed chest ischemia with first ligature-induction surgery and 3-7 d later 1 hour closed chest ischemia followed by 24 h reperfusion. Mice were sacrificed and hearts excised to perform spatial transcriptomic analysis on 10X Visium Gene Expression slides. The goal was to identify differences in gene expression between KO and control in the different zones of the heart after ischemia (eg. ischemic, border and remote zone).2026-02-28T00:00:00Z2026-02-28T02:02:26.261Z2023-03-02T11:44:29.069ZE-MTAB-12700ERP188967EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184