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Whole Cell Extract for Mouse Embryonic Fibroblasts

ABSTRACT: Mouse embryonic fibroblasts (MEFs) are an example of an early differentiated cell type. The whole cell extract was prepared in order to have background information for additional ChIP-Seq experiments in MEFs. The WCE data is a useful dataset that can be used as a background for many different analysis purposes.

ORGANISM(S): Mus musculus

PROVIDER: GSE22320 | GEO | 2010/06/15

SECONDARY ACCESSION(S): PRJNA127531

REPOSITORIES: GEO

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Whole Cell Extract for Mouse Embryonic Fibroblasts

Project description:Mouse embryonic fibroblasts (MEFs) are an example of an early differentiated cell type. The whole cell extract was prepared in order to have background information for additional ChIP-Seq experiments in MEFs. The WCE data is a useful dataset that can be used as a background for many different analysis purposes. MEFs were sonicated, DNA was purified and prepared for solexa sequencing.

2010-06-15 | E-GEOD-22320 | biostudies-arrayexpress

Effects of WCE herbal extract on hormone-refractory PC-3 tumors

Project description:Purpose: Androgen-deprivation therapy is the standard treatment for prostate cancer but fails in hormone-refractory prostate cancer. The anti-inflammatory plant Wedelia chinensis is rich in luteolin, apigenin, and wedelolactone that act synergistically to suppress androgen receptor activity in prostate cancer. Here, we evaluated the systemic antitumor effects of a standardized and effect-optimized Wedelia chinensis herbal extract (WCE) on hormone-refractory prostate cancer. Methods: Hormone-refractory PC-3 orthotopic tumor mouse models were orally administered with WCE. The tumor transcriptomes were studied using RNA sequencing and Ingenuity Pathway Analysis to identify the molecular mechanisms. Results: WCE significantly attenuated tumor growth and metastasis in orthotopic PC-3 xenografts. Transcriptomic analysis of genome-wide gene expression in the tumors revealed that WCE suppressed the expression of HIF1α, IKKα/β phosphorylation, and the downstream cytokines/chemokines. Conclusions: A standardized preparation of Wedelia chinensis improved prostate cancer therapy through repressing NFκB-mediated cytokine expression in tumor cells and modulating the inflammatory tumor microenvironment. These data suggest that WCE functions through immunomodulation and has potential application as an adjuvant agent for the treatment of castration-resistant prostate cancer.

2017-12-01 | GSE99820 | GEO

Transcritome analysis of herbal extract WCE mediated gene signature in 22Rv1 cells

Project description:Recurrences of hormone-refractory prostate cancer highly affect the therapeutic outcome. Although anti-androgen therapy prolongs survival in prostate cancer patients, resistance rapidly develops and is often associated with increased androgen receptor expression and upregulated HER2/3-AKT signaling pathway. However, single agent therapy targeting AR, HER2/3 or AKT usually failed due to the reciprocal feedback loop. Here, we demonstrated that herbal extract of Wedelia chinensis (WCE) effectively disrupted the androgen receptor, HER2/3, and AKT signaling network and therefore enhanced therapeutic efficacy of androgen ablation in PCa.

2017-06-21 | GSE100224 | GEO

Human Embryonic Stem Cells Polysomes

Project description:H1s are induced to differentiate into the trophoblast (TE) lineage, and polysome analysis performed at 0hr (Undifferentiated), 12hr TE and 24hr TE. The whole cell extract (WCE) is a cytoplasmic lysate of the cell . G1-G4 represent RNAs that were found in different fractions of a sucrose gradient, which represents monosomes, polysomes, etc. Thus the WCE is used as the denominator so that for a particular transcript, we can express G1, for example, as a fraction of the total RNA.

2014-07-21 | E-MTAB-1653 | biostudies-arrayexpress

A comparison of control samples for ChIP-seq of histone modifications

Project description:The advent of high-throughput sequencing has allowed genome wide profiling of histone modifications by Chromatin ImmunoPrecipitation (ChIP) followed by sequencing (ChIP-seq). In this assay the histone mark of interest is enriched through a chromatin pull-down assay using an antibody for the mark. Due to imperfect antibodies and other factors, many of the sequenced fragments do not originate from the histone mark of interest, and are referred to as background reads. Background reads are not uniformly distributed and therefore control samples are usually used to estimate the background distribution at any given genomic position. The Encyclopedia of DNA Elements (ENCODE) Consortium guidelines suggest sequencing a whole cell extract (WCE, or “input”) sample, or a mock ChIP reaction such as an IgG control, as a background sample. However, for a histone modification ChIP-seq investigation it is also possible to use a Histone H3 (H3) pull-down to map the underlying distribution of histones. In this paper we generated data from a hematopoietic stem and progenitor cell population isolated from mouse foetal liver to compare WCE and H3 ChIP-seq as control samples. The quality of the control samples is estimated by a comparison to pull-downs of histone modifications and to expression data. We find minor differences between WCE and H3 ChIP-seq, such as coverage in mitochondria and behaviour close to transcription start sites. Where the two controls differ, the H3 pull-down is generally more similar to the ChIP-seq of histone modifications. However, the differences between H3 and WCE have a negligible impact on the quality of a standard analysis.

2015-01-01 | GSE59419 | GEO

RNAseq changes in fibroblasts after treatment with selected protein(s) or E16.5 skin extract

Project description:Purpose: To identify the cellular processes upregulated in fibroblasts after treatment with selected protein(s) or E16.5 skin extract Methods: To explore the mechanism of extract-induced HF neogenesis, adult dermal fibroblasts were cultured in the presence of E16.5 extract or selected protein(s) for 3 days before being tested. Results: we determined how the exposure of adult fibroblasts to E16.5 extract, the selected protein mix or each of the selected proteins and compared the resultant transcriptomes with those of adult DP and embryonic dermal fibroblasts. Conclusions: Gene expression of adult fibroblasts exposed to E16.5 extract and selected proteins mix, the key DP signature genes became upregulated.

2016-08-10 | GSE85303 | GEO

RNAseq changes in human fibroblasts after treatment with E16.5 skin extract

Project description:To identify the cellular processes upregulated in fibroblasts after treatment with E16.5 skin extract

2017-02-24 | GSE95245 | GEO

Hepatic gene expression profile in persimmon peel extract administrated GK rat

Project description:Persimmon (Diospyros kaki L. f.) is a most popular fruit in Asian countries but its peels are totally wasted despite of containing a plenty of antioxidants such as carotenoids and polyphenols. We prepared a fat-soluble extract from a persimmon peel (PP) fraction and fed type 2 diabetic Goto-Kakizaki (GK) rats with a PP extract-containing AIN-93G diet (PP diet) for 12 weeks. Compared with the control AIN-93G diet, the feeding of the PP diet reduced the plasma glutamic-pyruvate transaminase activity significantly, with accumulation of β-cryptoxanthin in the liver. A DNA microarray analysis revealed that the PP diet altered the hepatic gene expression profiles. In particular, insulin signaling pathway-related genes were significantly enriched in differentially expressed gene sets. Moreover, Western blotting analysis actually showed the promotion of IRβ tyrosine phosphorylation. All these data suggest that the PP extract administration to the GK rats improves their insulin resistance.

2011-03-17 | GSE21417 | GEO