Inflammation & Metabolism Shiny Apps

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We regularly download and process public data for our various projects related to skeletal muscle adaptation to exercise, metabolic diseases and inflammation. This server provides access to all the data in the form of shiny apps to easily interrogate the different datasets.

Nicolas J. Pillon, PhD

Assistant Professor, Docent
Department of Physiology and Pharmacology
Karolinska Institutet
Solnavägen 9, C4
171 77 Stockholm, Sweden
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nicolas.pillon@ki.se
+46 (0)8-524 875 12
http://nicopillon.com

Inflammation & Metabolism

Skeletal Muscle

IMPORTANT: The datasets presented here are updated regularly and without notice. Do not use the figures presented here for publication as they will lack reproducibility. Contact me so that we define precisely the adequate methods for you and make the best figures for publication.

MetaMEx

The famous meta-analysis of the transcriptomic response of skeletal muscle to exercise and inactivity. Published in 2020 and regularly updated with the most recent transcriptomic datasets.

Pillon et al. Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity. Nat Commun. 2020 Jan 24;11(1):470.

Skeletal Muscle Cells and Tissues

Manually curated database of skeletal muscle tissue compared to the 3 most commonly used in vitro models: mouse C2C12, rat L6 and human primary myotubes. Published in 2020 and recently updated with RNA sequencing data.

Abdelmoez et al. Comparative profiling of skeletal muscle models reveals heterogeneity of transcriptome and metabolism. Am J Physiol Cell Physiol. 2020 Mar 1;318(3):C615-C626.

Synchronized Myotubes Exposed to Glucose or Palmitate

RNA sequencing analysis of primary human myotubes from individuals with T2D or healthy controls. Cell were synchronized and exposed to either palmitate or high glucose concentration for up to 54h. App developed by Laura Sardon Puig and Mladen Savikj.

Gabriel et al. Disrupted circadian oscillations in type 2 diabetes are linked to altered rhythmic mitochondrial metabolism in skeletal muscle. Sci Adv. 2021 Oct 22;7(43):eabi9654.
Pillon, Sardón Puig et al. Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers. Life Sci Alliance. 2022 Oct 27;6(1):e202201598.

Myoblast-to-myotube Differentiation and T2D

Analysis of 2 datasets of myoblasts/myotubes grown from healthy controls or individuals with type 2 diabetes.

GSE55650 - Brown et al. p38 MAPK activation upregulates proinflammatory pathways in skeletal muscle cells from insulin-resistant type 2 diabetic patients. Am J Physiol Endocrinol Metab 2015 Jan 1;308(1):E63-70. https://doi.org/10.1152/ajpendo.00115.2014
GSE166502 - Davegårdh et al. VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics. Nat Commun 2021 Apr 23;12(1):2431. https://doi.org/10.1038/s41467-021-22068-5

Palmitate Exposure

Datasets of skeletal muscle cells exposed to the saturated fatty acid palmitate.

Electrical Pulse Stimulation

Datasets of skeletal muscle cells exposed to electrical pulse stimulation.

Heterogeneity of Myotubes From Different Donors

Transcriptomic description of the cells grown in the integrative physiology lab at Karolinska Institutet.

AMPK-mutant Mice

Manually curated database of skeletal muscle tissue from mice with modulation of AMPK through knockout, mutation or AICAR stimulation. Dataset includes transcriptomic data from a1, a2, a1a2 and g3 knockout mice, g3 transgenic and AICAR stimulation for 6-14 days (pooled datasets).

Hyperinsulinemic euglycemic clamp

Manually curated database of skeletal muscle response to hyperinsulinemic euglycemic clamp. The analysis incudes 3 studies performed in healthy individual as well as participants with insulin resistance or diabetes. The studies collected biopsies after 30, 120, 180 and 240 minutes during the clamp.

Skeletal Muscle Injury

Analysis of 5 datasets in mouse models of skeletal muscle injury and exercise. The studies include samples collected over 24h after injuries induced by either freeze, blunt, incision or eccentric contractions. A dataset of treadmill exercise is included for comparison.

Single cell RNAseq of acute exercise

Data from human biopsies before and after an acute bout of exercise.

Lovric et al. Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle. Commun Biol. 2022 Oct 22;5(1):1121.

Immune cells

Macrophage Polarization

Manually curated database of human and mouse macrophages differentiated in vitro and polarized into M1 and M2 phenotype. The database also includes macrophages isolated from human adipose tissue and sorted based on CD11c expression by FACS from Acosta et al. 2017.

Immune Populations in Human Adipose Tissue

Transcriptomic data from cells isolated from human adipose tissue by FACS. From:

GSE80654 - Ehrlund et al. The cell-type specific transcriptome in human adipose tissue and influence of obesity on adipocyte progenitors. Sci Data 2017 Oct 31;4:170164.
GSE100795 - Acosta et al. Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population. J. Stem Cell Res Ther. 2017 Nov 7;8(1):250.

Obesity

Mouse Obesity Transcriptomics

Gene expression in tissues from high fat fed mice.

Human Obesity Transcriptomics

Gene expression in tissues from individuals with obesity.

miRNAs

miRNA in circulating EVs after acute exercise

Meta-analysis of miRNA found in circulating extracellular vesicules before and after an acute bout of exercise.