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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis through inhibition of Wnt signaling

ABSTRACT: The developmental transcription factor SOX6 was found to regulate serum, as well as liver triglycerides in BL6 mice treated with SOX6 antisense gapmers compared to control gapmers. SOX6 was initially discovered as a gene over-expressed in mesenchymal stem cells derived from small for gestational age newborns. We characterized its metabolic function in BL6 mice using the above antisense knockdown approach. BL6 mice were treated with either SOX6 specific or control gapmer oligonucleotides for 48h. Knockdown efficiency was measured in liver and epididymal white adipose tissues and serum levels of triglycerides and cholesterol quantified.

ORGANISM(S): Mus musculus

SUBMITTER: Walter Stunkel

PROVIDER: E-GEOD-70300 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis through inhibition of Wnt signaling

Project description:The developmental transcription factor SOX6 was found to regulate serum, as well as liver triglycerides in BL6 mice treated with SOX6 antisense gapmers compared to control gapmers. SOX6 was initially discovered as a gene over-expressed in mesenchymal stem cells derived from small for gestational age newborns. We characterized its metabolic function in BL6 mice using the above antisense knockdown approach.

2015-06-26 | GSE70300 | GEO

Long Non-Coding RNA MEG3 Promotes Angiogenesis by directly regulating integrin signaling impairing endothelial cell function [ChIP-seq]

Project description:We immunoprecipitated EZH2, together with associated chromatin isolated from the HUVECs (2 x 10^6) that were transfected with MEG3 GapmeRs (10 nM, 48 h) or a scrambled control GapmeRs (Ctr). For transfection, we used 10 nM scrambled LNA (locked nucleic acids) GapmeR control (Cat. No. 339515) or phosphorothioate antisense standard GapmeRs MEG3-lncRNA (Cat No. 339511, Qiagen). On beads crosslinked chromatin complexes were reversed, and DNA purified using QIAquick® PCR Purification Kit and quantified by Qubit HS assay (Q33230)

2024-04-12 | GSE234543 | GEO

Gene expression analysis in liver collected from mice administered non-toxic, toxic, or severely toxic LNA sequences

Project description:Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice receiving non-toxic and toxic LNA gapmers after a single and repeat administration. To understand the mechanism of LNA gapmer-induced heptotoxicity in mice, we investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1), toxic sequence (TS-2), or severely toxic sequence (HTS-3) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 8, 16, or 72 hrs after a single administration (by subcutaneous injection ) using microarray analysis. We also investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1) or toxic sequence (TS-2) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 2 weeks after repeated administration (by subcutaneous injection ) using microarray analysis.

2014-01-08 | E-GEOD-53230 | biostudies-arrayexpress

CUT&RUN HUDEP1 OE SOX6-Flag

Project description:SOX6 CUT&RUN on HUDEP1 over expressing SOX6-Flag. The experiment is done using and anti Flag Ab to assist the genome wide binding profile of SOX6 in HUDEP1 (Human Umbilical cord blood-Derived Erythroid Progenitor-1).

2023-04-07 | E-MTAB-12800 | biostudies-arrayexpress

Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes

Project description:In order to understand how Sox6 coordinately regulates the transcription of multiple fiber type specific genes during muscle development, we have performed ChIP-seq analyses to identify Sox6 target genes as well as RNA polymerase II (Pol II) binding sites in mouse fetal myotubes. Examination of Sox6 and Pol II binding sites in mouse fetal primary myotubes

2011-10-06 | E-GEOD-32627 | biostudies-arrayexpress

Genome-wide mapping of Sox6 binding sites in mouse fetal myotubes

2011-10-06 | GSE32627 | GEO

Illumina Microarray of T47D cell with or without KDM7A-DT silencing under normal and oxidative stress conditions

Project description:KDM7A Divergent Transcript (KDM7A-DT) is a stress-induced lncRNAs. In our previous studies, KDM7A-DT showed the most robust cellular phenotype alteration and a significant TP53-dependency upon oxidative and oncogenic stress induction. Since about 50% of human breast cancers have mutant p53 and associated genetic alterations, it is essential to determine what effect a mutant p53 would have on acquired pro-oncogenic functions of KDM7A-DT. In these experiments, we used four antisense LNA Gapmer sequences designed by Exiqon (Vedbaek, Denmark). One of these was a negative control, while the other 3 were designed to target the end of the transcript representing the full-length lncRNA KDM7A-DT (lncRNA; GRCh38/hg38, chr7: 140,178,951-140,179,640). To test the effect of KDM7-DT in the context of mutant p53, we selected the p53-negative luminal BC cells T47D. For each of the LNA gapmers, we utilized 3 technical replicates across two main experimental conditions (normal vs. oxidative stress induced via 30 mins of 0.2 mM H2O2 treatment). Overall, we measured the signals for 47,323 Illumina array probes across 24 individual experiments (4 LNA gapmers * 3 technical replicates * 2 main experimental conditions).

2023-05-01 | E-MTAB-11818 | biostudies-arrayexpress

Sox5 and Sox6 direct a cardiac adaptive response to pressure overload

Project description:Rationale: We previously demonstrated that the transcription factor Sox6 regulates skeletal muscle biology by determining myofiber composition and muscle performance. Although the role of Sox6 and Sox5, its closest paralog, has not been ascertained in the heart, genome-wide association studies linked both Sox5 and Sox6 to cardiovascular disease. Objective: This study identifies the role of Sox5 and Sox6 in the adult mammalian heart under normal and stress conditions. Methods and Results: Using Sox5 and Sox6 cardiac-specific and Sox5 conduction system-specific knockout mice, we investigated the role of the two transcription factors in the heart under normal conditions and during cardiac stress. Sox5/6-deficient (DKO) mice displayed blunted cardiac contractility, which was present in Sox5 but not Sox6 single KO mice. DKO mice had a mild reduction in blood pressure, and conduction-specific knockout of Sox5 resulted in a reduced heart rate at baseline. After cardiac pressure overload, DKO mice showed increased lethality compared to control mice and were more prone to develop heart failure. We performed RNA deep sequencing in ventricles from DKO and control mice to identify potential Sox5/6 target genes and found altered expression of genes encoding regulators of calcium handling and cation transporters. Patch-clamping in isolated cardiomyocytes revealed shortened action potential duration in Sox5 KO cells. Conclusions: Unlike in skeletal muscle, our results suggest Sox5 but not Sox6 to be a major regulator of cardiac function and rhythm. Sox5 is essential to preserve cardiac function under normal conditions by maintaining contractility and to prevent cardiac failure after pressure overload.

2018-08-05 | GSE60538 | GEO

Knockdown of circular RNAs using LNA-modified antisense oligonucleotides

Project description:Circular RNAs (circRNAs) constitute an abundant class of covalently closed non-coding RNA molecules that are formed by backsplicing from eukaryotic protein-coding genes. Recent studies have shown that circRNAs can act as microRNA or protein decoys as well as transcriptional regulators. However, the functions of most circRNAs are still poorly understood. Because circRNA sequences overlap with their linear parent transcripts, depleting specific circRNAs without affecting host gene expression remains a challenge. Here, we assessed the utility of LNA-modified antisense oligonucleotides (ASOs) to knock down circRNAs for loss-of-function studies. We identified 5807 circRNAs in total RNA sequencing data from 4 liver cancer cell lines and used the back splice junction (BSJ) sequences of 7 validated circRNAs as target sites for designing different LNA-modified ASOs for circRNA knockdown. We found that while most RNase H-dependent gapmer ASOs mediate effective knockdown of their target circRNAs, some gapmers reduce the levels of the linear parent transcript and may also cause degradation of unintended off-targets. The circRNA targeting specificity can be enhanced using design-optimized gapmer ASOs or LNA/DNA mixmer ASOs, which display potent and specific circRNA knockdown with a minimal effect on the host genes or predicted off-targets. In summary, our results demonstrate that LNA-modified ASOs complementary to BSJ sequences mediate robust knockdown of circRNAs in vitro and, thus, represent a useful tool to explore the biological roles of circRNAs in loss-of-function studies in cultured cells and animal models.

2022-11-01 | GSE145592 | GEO

Gene expression and exon splicing of two Ewing sarcoma cell lines (TC-32, RDES), transiently transfected with shControl or two different shRNA against SOX6

Project description:In this dataset, we include the gene expression and exon splicing variants of two Ewing sarcoma cell lines (RDES and TC-32) after knockdown of the transcription factor SOX6 in order to obtain differentially expressed genes and different exon splicing variants.

2020-04-01 | GSE120576 | GEO

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