Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Cardiac microRNA profiling in mice treated with lipopolysacharide

ABSTRACT: To identify the microRNA (miR) profile in the hearts of mice that were treated with lipopolysaccharide (LPS) and compare this profile with respective profiles that have been published in studies with mice that underwent pressure overload heart failure, 8 mouse samples were hybridized to Sanger 14 Multi-Species miR microarrays. As a result, we observed that particular cardiac miRs that are modulated during pressure overload heart failure are not affected significantly by treatment with LPS Total RNA from pieces of hearts obtained from 8 C57BL/6 mice that were treated either with saline (4 mice) or with lipopolysacharide (4 mice).

ORGANISM(S): Mus musculus

SUBMITTER: Konstantinos Drosatos

PROVIDER: E-GEOD-29914 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Inhibition of c-Jun-N-terminal kinase increases cardiac peroxisome proliferator-activated receptor alpha expression and fatty acid oxidation and prevents lipopolysaccharide-induced heart dysfunction.

Drosatos Konstantinos K Drosatos-Tampakaki Zoi Z Khan Raffay R Homma Shunichi S Schulze P Christian PC Zannis Vassilis I VI Goldberg Ira J IJ

The Journal of biological chemistry 20110826 42

Septic shock results from bacterial infection and is associated with multi-organ failure, high mortality, and cardiac dysfunction. Sepsis causes both myocardial inflammation and energy depletion. We hypothesized that reduced cardiac energy production is a primary cause of ventricular dysfunction in sepsis. The JNK pathway is activated in sepsis and has also been implicated in impaired fatty acid oxidation in several tissues. Therefore, we tested whether JNK activation inhibits cardiac fatty acid ...[more]

PMID: 21873422

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Project description:We developed cell2location, a principled and versatile Bayesian model that is designed to resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. To validate cell2location in real tissue, we applied the model to data from the mouse brain, which features diverse neural cell types organised in a well characterised spatial architecture across brain areas, thus presenting a canonical use case to test spatial genomics. We generated matched single nucleus (sn, this submission) and Visium spatial RNA-seq (10X Genomics) profiles of adjacent mouse brain sections that contain multiple regions from the telencephalon and diencephalon. To assess the biological and intra-organ technical variation in spatial mapping, we assayed two mouse brains and serial tissue sections from each brain (total of 3 and 2 matched sections from two animals, respectively, and an extra section for snRNA-seq), creating a rich multi-modal and replicated transcriptomic dataset. Tissue processing. Brains of wild-type adult C57BL/6 mice (postnatal day 56, 1 female and 1 male) were dissected, snap frozen, embedded in optimal cutting temperature compound (Tissue-Tek) and stored at -80oC. Brain hemispheres were cryosectioned at -20oC using a cryostat (Leica, CM3050S). To assess tissue quality, RNA was extracted from test tissue sections using the RNeasy Pico Kit (Qiagen) and yielded high RIN values (9.6 and 9.7) on an Agilent Bioanalyser, indicating high RNA quality. For matched single nuclei and Visium RNA-seq experiments, brain hemispheres were cryosectioned to adjacent thick (200 µm) and thin (10 µm) coronal sections, respectively, and processed the same day. In total, four consecutive sets of thick and thin tissue sections were collected from each brain. Five sets of tissue sections yielded both good quality single nuclei and Visium data (three adjacent sections from mouse 1 and two sections from mouse 2) while one additional section from mouse 2 yielded good single nuclei; these were considered for analysis in this study. Single nucleus RNA-sequencing. Thick (200 µm) mouse brain sections were cryosectioned, dissected from OCT and kept in a tube on dry ice until subsequent processing. Nuclei were extracted from each section as described previously. Briefly, nuclei were released from sections via Dounce homogenisation, Hoechst-stained, and isolated via fluorescence-activated cell sorting (FACS). Nuclei were then loaded into the 10X Chromium Single Cell 3′ Kit (v3) to obtain 3,000-7,000 nuclei per well, and library preparation was done per manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq S4 system. Sequencing data were processed using 10X CellRanger version 3.0.2, aligned to mouse pre-mRNA genome reference version mm10 and mRNA count matrices were generated by adding intronic and exonic unique molecular identifier (UMI) counts for each gene in each cell. Initially, snRNA-seq counts were processed using standard Seurat V3 workflow without correcting batch effects between 6 individual samples.

Dataset Information

Cardiac microRNA profiling in mice treated with lipopolysacharide

Publications

Inhibition of c-Jun-N-terminal kinase increases cardiac peroxisome proliferator-activated receptor alpha expression and fatty acid oxidation and prevents lipopolysaccharide-induced heart dysfunction.

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