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Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from SGBS human cells before and after 24 hours of stimulation with differentiation cocktail, with or without Scrambled (Scr) or Tenomodulin (TNMD) siRNA to knockdown the genes of interest.

ABSTRACT: In a screen for upregulated adipocyte genes in insulin resistant versus insulin sensitive subjects matched for BMI, we identified the type II transmembrane protein tenomodulin (TNMD), previously implicated in glucose tolerance in gene association studies. TNMD expression was greatly increased in human preadipocytes during differentiation, while silencing TNMD blocked adipogenic gene induction and adipogenesis. We used microarrays to identify genes of interest that are differentially expressed after the addition of siRNA to tenomodulin or scrambled siRNA, in both preadipocytes and partially differentiated adipocytes. SGBS preadipocytes were treated with scrambled or siTNMD. Cells either were kept undifferentiated or stimulated for 24 hours with differentiation cocktail. Cells were prepared with this protocol on three different occasions and total RNA was isolated to provide three biological replicates per sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Michael Czech

PROVIDER: E-GEOD-76319 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from SGBS human cells before and after 24 hours of stimulation with differentiation cocktail, with or without Scrambled (Scr) or Tenomodulin (TNMD) siRNA to knockdown the genes of interest.

Project description:In a screen for upregulated adipocyte genes in insulin resistant versus insulin sensitive subjects matched for BMI, we identified the type II transmembrane protein tenomodulin (TNMD), previously implicated in glucose tolerance in gene association studies. TNMD expression was greatly increased in human preadipocytes during differentiation, while silencing TNMD blocked adipogenic gene induction and adipogenesis. We used microarrays to identify genes of interest that are differentially expressed after the addition of siRNA to tenomodulin or scrambled siRNA, in both preadipocytes and partially differentiated adipocytes.

2016-02-11 | GSE76319 | GEO

LSD1 knockdown in 3T3-L1 preadipocytes

Project description:Obesity is often associated with a low-grade systemic inflammation state that contributes to the development of insulin resistance and atherosclerotic complications. This is usually coupled with increased macrophage infiltration in the adipose tissue and a defect in adipocyte differentiation that results in accumulation of hypertrophic fat cells characterized by a deregulated pattern of adipokine expression. Here we show that knockdown of histone demethylase lsd1 in 3T3-L1 preadipocytes results in defective adipogenesis and derepression of an inflammatory program in these cells. The dataset consists of four sample groups: [1] 3T3-L1 preadipocytes (passage 19) transfected with a control scrambled siRNA at 24h after transfection (siC.24h), [2] 3T3-L1 preadipocytes (p.19) transfected with a siRNA directed against LSD1 at 24h after transfection (siLsd1.24h), [3] 3T3-L1 preadipocytes (p.21) transfected with a control scrambled siRNA at 48h after transfection (siC.48h), and [4] 3T3-L1 preadipocytes (p.21) transfected with a siRNA directed against LSD1 at 48h after transfection (siLsd1.48h). The 24h sample groups (siC.24h and siLsd1.24h) consist of two biological replicate samples; the 48h sample groups (siC.48h and siLsd1.48h) consist of three biological replicate samples. Each sample was hybridized to a separate array, for a total of ten arrays.

2013-12-31 | E-GEOD-25423 | biostudies-arrayexpress

Adverse Effects of Bisphenol A and its substitute compounds on human SGBS preadipocytes

Project description:Bisphenol A (BPA), which is used in a variety of consumer-related plastic products, was reported to cause metabolic disruption. Substitute compounds are increasingly emerging, but are not sufficiently investigated. In this study, we aimed to investigate the mode of action of BPA and four of its substitutes during the differentiation of human preadipocytes. Human preadipocytes were exposed to BPA, BPS, BPB, BPF, and BPAF, as well as the PPARγ-antagonist GW9662. After 12 days of differentiation, global protein profiles were assessed using LC-MS/MS-based proteomics.

2021-08-05 | PXD023227 | Pride

Proteomic characterization of SGBS cells

Project description:In this study, SGBS preadipocytes were differentiated for 12 days into mature preadipocytes.

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Expression data from human SGBS adipocytes under hypoxic conditions

Project description:Hypoxia in adipose tissue is suggested to be involved in the development of a chronic mild inflammation, which in obesity can further lead to insulin-resistance. The effect of hypoxia on gene expression in adipocytes seems to play a central role in this inflammatory response observed in obesity. However, the global impact of hypoxia on transcriptional changes in human adipocytes is unclear. Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays. Human SGBS adipocytes were cultured in a hypoxic environment (1% O2) for 3, 6 and 16 hours and the control group was cultured under normoxic conditions (21% O2). Total RNA was prepared from control and treated SGBS cells, in triplicate experiments, and probes were hybridized on ‘Human Genome U133 2.0’ arrays (Affymetrix).

2011-04-14 | E-GEOD-28603 | biostudies-arrayexpress

Massively parallel reporter assays (MPRAs) of 175bp human genomic fragments containing variants in high LD with lead variants from obesity GWAS associations.

Project description:We performed a massively parallel reporter assay on 2,396 genomic regions containing single nucleotide polymorphisms that are in high linkage disequilibrium with 97 lead variants from an obesity GWAS (PMID: 25673413). Regions were transfected into human SGBS preadipocytes, SGBS mature adipocytes, 3T3-L1 preadipocytes, HT22 hippocampal cells, and GT1-7 cells and assessed for enhancer activity. The processed file contains the MPRA barcodes.

2021-05-22 | E-MTAB-10463 | biostudies-arrayexpress

In situ promoter capture Hi-C data of differentiated SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)

Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for in situ promoter capture Hi-C [PMID: 29988018] at several differentiation stages. The differentiations were performed in one biological replicate, with two technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.

2021-05-29 | E-MTAB-10488 | biostudies-arrayexpress

Proteome dynamics during differentiation of SGBS adipocytes

Project description:Here, we identified temporal dynamics in the proteome during adipocyte differentiation of the human SGBS cells, applying untargeted proteomics. Samples were taken at initiation of differentiation, at an intermediate and terminal time point.

2024-06-13 | PXD045767 | Pride

Acetylome dynamics during differentiation of SGBS adipocytes

Project description:Here, we identified temporal dynamics of the acetylome during adipocyte differentiation in human SGBS cells, applying untargeted proteomics in combination with immunoaffinity purification of acetylated peptides. Samples were taken at initiation of differentiation, at an intermediate and terminal time point.

2024-06-13 | PXD045768 | Pride

Gene expression profiling (RNA-seq) of SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)

Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for RNA-seq at several differentiation stages. The differentiations were performed in one biological replicate, with three technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.

2021-05-22 | E-MTAB-10461 | biostudies-arrayexpress

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