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Series GSE138940 Query DataSets for GSE138940
Status Public on Dec 30, 2019
Title Muscle specific MyD88-/- confers a sexual dimorphism protecting female mice from inactivity-induced fat accumulation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We demonstrate whole body inflammation (miR146a-/-) exacerbated inactivity-induced fat gain and glucose dysregulation, while muscle specific MyD88 KO mitigated these outcomes in female mice. Higher gene expression of Igf1 and decreased expression of Ip6k3 in muscle of MyD88 KO female mice may explain enhancement of glucose uptake in the soleus. Whereas protection from fat accumulation may be related to visceral fat gene changes in adipose tissue expansion (Prc1↓, Gulp1↑, Anxa2↓, Cav2↓, EHD1↓), adipose beiging (Fgf10↑), metainflammation (Hmox1↓), and genes involved in perfusion. Of noteworthy to mention, two genes decreased in common between muscle and fat with the ablation of muscle MyD88. These were expression of the negative regulator for GLUT4 translocation, Ralgapa2, and uncharacterized 993011J21Rik2, a potential interferon interacting gene. We conclude that future therapeutic strategies for prevention or treatment of obesity and metabolic disturbances in populations unable to be physically active should focus on further understanding how skeletal muscle inflammation communicates with fat storage depots, and how this cross-talk is influenced by sex hormones.
Overall design Total RNA was isolated from visceral fat and the red portion of the gastrocnemius muscle as described previously (25). Briefly, tissue was homogenized in Tri Reagent LS (Molecular Research Center, Cincinnati, OH, USA) and disrupted via hand-held homogenizer (Bio-Gen PRO200; Pro Scientific, Oxford, CT, USA). Chloroform separation was used and RNA was precipitated using isopropanol. RNA was purified using TURBO DNase (AM2238) with Zymo RNA Clean and Concentrator-5 clean up. RNA sequencing and library construction was performed by the University of Utah High Throughput Genomics Core. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples. Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371). Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583), and average RIN was 8.3. The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824). Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis. Sequencing libraries (1.3 nM) were chemically denatured and applied to an Illumina NovaSeq flow cell using the NovaSeq XP chemistry workflow (20021664). Following transfer of the flowcell to an Illumina NovaSeq instrument, a 2 x 51 cycle paired end sequence run was performed (NovaSeq 2 x 50 bp Sequencing_100 M Read-Pairs) using a NovaSeq S1 reagent Kit (20027465).
Contributor(s) Mahmassani ZS, Reidy PT, McKenzie AI, Petrocelli JJ, Matthews O, de Hart N, Ferrara PJ, O'Connell R, Funai K, Drummond MJ
Citation(s) 32108446
Submission date Oct 16, 2019
Last update date Jul 02, 2020
Contact name Micah J Drummond
Organization name The University of Utah
Department Physical Therapy and Athletic Training
Lab Drummond Lab
Street address 520 Wakara Way
City Salt Lake City
State/province Utah
ZIP/Postal code 84108
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (16)
GSM4123953 16149X1 131-M
GSM4123954 16149X2 137-M
GSM4123955 16149X3 138-M
BioProject PRJNA577857
SRA SRP225890

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GSE138940_counts_raw.txt.gz 706.5 Kb (ftp)(http) TXT
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