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SRX11243530: GSM5403849: primary hepatocytes, butyric acid treatment, replicate 1; Mus musculus; RNA-Seq
1 BGISEQ (BGISEQ-500) run: 46.4M spots, 7G bases, 4.2Gb downloads

Submitted by: NCBI (GEO)
Study: RNA-sequencing reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes
show Abstracthide Abstract
Various forms of fasting, including time-restricted feeding, alternate day fasting, and periodic fasting have shown promise in clinical and pre-clinical studies to normalize body weight, improve metabolic health, and protect against disease. Recent studies suggest that ß-hydroxybutyrate (ßOHB), a characteristic ketone body of the fasted metabolic state, acts as a potential signaling molecule mediating the beneficial effects of the various forms of fasting, potentially by acting as a histone deacetylase inhibitor. In the first part we investigated whether ßOHB, in comparison to the well-established histone deacetylase inhibitor butyrate, influences cellular differentiation in vitro. In C2C12 myotubes, 3T3-L1 adipocytes, and THP-1 monocytes, millimolar concentrations of ßOHB did not alter differentiation, as determined by gene expression and histological assessment, whereas equimolar concentrations of butyrate potently impaired differentiation in all cell types. RNA-sequencing revealed that unlike butyrate, ßOHB minimally impacted gene expression in adipocytes, macrophages, and hepatocytes. However, in myocytes, ßOHB upregulated genes involved in the TCA cycle and oxidative phosphorylation, while downregulating genes belonging to cytokine and chemokine signal transduction. Overall, our data do not support the notion that ßOHB serves as a powerful signaling molecule regulating gene expression in adipocytes, macrophages and hepatocytes, but suggest that ßOHB may act as a niche signaling molecule in muscle. Overall design: Mouse primary cells (adipocytes, macrophages, skeletal myotubes, hepatocytes) were exposed to ß-hydroxybutyric acid (bOHB; 5mM), butyric acid (5mM), or control treatment, and subjected to gene expression profiling by RNA-sequencing.
Sample: primary hepatocytes, butyric acid treatment, replicate 1
SAMN19945841 • SRS9338339 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: BGISEQ-500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Total RNA from all cell culture samples was extracted using TRIzol reagent (Thermo Fisher Scientific) and purified using the Qiagen RNeasy Mini kit (Qiagen) according to manufacturer's instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies). Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).
Experiment attributes:
GEO Accession: GSM5403849
Links:
Runs: 1 run, 46.4M spots, 7G bases, 4.2Gb
Run# of Spots# of BasesSizePublished
SRR1493072646,444,6967G4.2Gb2021-08-12

ID:
15012324

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