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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effect of p53 in human iPS cell generation

ABSTRACT: p53 knockdown by shRNA markedly increased efficiency of human iPS cell generation Gene expression patterns were compared between human ES cells and dermal fibroblasts. Gene expression patterns were also compared between p53 shRNA-treated fibroblasts and control fibroblasts.

ORGANISM(S): Homo sapiens

SUBMITTER: Shinya Yamanaka

PROVIDER: E-GEOD-13334 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Suppression of induced pluripotent stem cell generation by the p53-p21 pathway.

Hong Hyenjong H Takahashi Kazutoshi K Ichisaka Tomoko T Aoi Takashi T Kanagawa Osami O Nakagawa Masato M Okita Keisuke K Yamanaka Shinya S

Nature 20090809 7259

Induced pluripotent stem (iPS) cells can be generated from somatic cells by the introduction of Oct3/4 (also known as Pou5f1), Sox2, Klf4 and c-Myc, in mouse and in human. The efficiency of this process, however, is low. Pluripotency can be induced without c-Myc, but with even lower efficiency. A p53 (also known as TP53 in humans and Trp53 in mice) short-interfering RNA (siRNA) was recently shown to promote human iPS cell generation, but the specificity and mechanisms remain to be determined. He ...[more]

PMID: 19668191

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Effect of p53 on iPS cell generation

Project description:This SuperSeries is composed of the following subset Series: GSE13312: Role of p53 in mouse iPS cell generation GSE13334: Effect of p53 in human iPS cell generation Refer to individual Series

2009-02-28 | E-GEOD-13365 | biostudies-arrayexpress

Myc-regulated gene expression in human fibroblasts

Project description:Myc regulates many gene expression during cell growth, development, or other many cellular events. C-Myc is a well known molecule which expression increase in many cancers. Overexpression of c-Myc causes cell transformation, apoptosis, etc. There are several Myc family genes in human, mouse, or other species. The function of N-Myc was well characterized and was similar to that of c-Myc. However, the function of L-Myc is not clearly examined. To examine the function of L-Myc, we perfomed microarray analyses using L-Myc overexpressed human fibroblasts. Adult human fibroblasts were transduced with Myc and their mutants and were used for microarray analyses.

2010-07-26 | E-GEOD-22654 | biostudies-arrayexpress

Differences in the transcriptomes of organically and conventionally grown potatoes.

Project description:Microarray analysis was performed on a well-defined set of potato tuber samples grown under different, well-recorded environmental conditions. The data were analysed to assess the potential of transcriptomics to detect differences in gene expression as a result of these environmental conditions. Differences were found for both factors, both in PCA and in ANOVA analysis.

2011-12-31 | E-MTAB-605 | biostudies-arrayexpress

Root transcriptome remodeling of Arabidopsis in response to high levels of magnesium sulfate

Project description:Martian regolith (unconsolidated surface material) is a potential medium for plant growth in bioregenerative life support systems during manned missions on Mars. However, hydrated magnesium sulfate mineral levels in the regolith of Mars can reach as high as 10 wt%, and would be expected to be highly inhibitory to plant growth. A global approach was used to identify novel genes with potential to enhance tolerance to high MgSO4 stress. The early Arabidopsis root transcriptome response to elevated concentrations of magnesium sulfate was characterized in col-0, and also between col-0 and the mutant line cax1-1 – a mutant relatively tolerant of high levels of MgSO4•7H2O in soil solution. After 3 weeks of growth under hydroponic conditions, Arabidopsis thaliana col-0 roots were exposed to a basic nutrient solution (0.25 g/L MES, 1/16x MS, pH 5.7) with an additional 2.08 mM magnesium sulfate (total Ca:Mg ratio = 1:15) for 45 min., 90 min., or 180 min., while a col-0 control set was exposed to the basic nutrient solution without additional magnesium sulfate for 45 minutes. Arabidopsis thaliana cax1-1 roots were exposed to the basic nutrient solution with additional magnesium sulfate for 180 min. only. Four replicate containers were harvested for the control and each of the treatment sets, resulting in a total of 20 samples. Gene expression of the col-0 sets exposed to magnesium sulfate treatment for 45 min., 90 min., or 180 min. was compared to gene expression of the col-0 control set. Gene expression of the cax1-1 set exposed to magnesium sulfate treatment for 180 min. was compared to gene expression of the col-0 set exposed to magnesium sulfate treatment for 180 minutes.

2010-09-17 | E-GEOD-20109 | biostudies-arrayexpress

Expression analysis of meristematic tissue (Me) and young leaves (Le) isolated by manual dissection of clv3-9 plants

Project description:For the expression analysis of undifferentiated and differentiated tissues a meristem enriched fraction and young leaves (up to 3 mm leaf blade length) were isolated from clavata3-9 plants. Clavata3-9 mutants harbour larger shoot apical meristems than wild type plants enabling the preparation of meristematic tissue by manual dissection. Samples from both tissues were used for expression and histone H3 lysine 27 trimethylation (H3K27me3) analysis. Tissues for expression and H3K27me3 ChIP-chip analyses were simultaneously harvested. Meristem enriched samples (XMe1 and XMe2) and young leaf samples (XLe1 and XLe2) of clavata3-9 plants were isolated and hybridised to Agilent 44 k arrays [G2519F, V4 (Agilent, Santa Clara)]. Two biological replicates were performed.

2011-03-21 | E-GEOD-24464 | biostudies-arrayexpress

Transcriptome profiling of a bendiocarb resistant strain of Anopheles gambiae in Cameroon

Project description:Transcriptome profiling of a bendiocarb resistant strain of Anopheles gambiae in Cameroon (S form) compared to the susceptible strain Kisumu (S form)

2014-03-18 | E-MTAB-1563 | biostudies-arrayexpress

Transcription profiling of mouse wild type and p53-null embryonic fibroblasts and stem cells

Project description:We observed a marked increase in efficiency of iPS cell generation when p53 is deleted. Experiment Overall Design: Gene expression patterns were compared between p53 wt MEF and p53-null MEF cells. Experiment Overall Design: Gene expression patterns were also compared between ES cells and MEF.

2009-04-10 | E-GEOD-13312 | biostudies-arrayexpress

Transcriptional responses of human monocyte-derived macrophages (HMDM) to lipopolysaccharide (LPS)

Project description:Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing inter-species differences in the transcriptional responses of primary human and mouse macrophages to the TLR4 agonist, LPS. Using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5M-bM-^@M-^Y ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologs, http://www.macgate.qfab.org). Divergently regulated (DR) orthologs were enriched for genes encoding cellular M-bM-^@M-^\inputsM-bM-^@M-^] such as cell surface receptors (e.g. TLR6, IL-7RM-NM-1), and functional M-bM-^@M-^\outputsM-bM-^@M-^] such as inflammatory cytokines/chemokines (e.g. CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. DR genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced inter-species promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change. Human monocyte-derived macrophages (HMDM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 2, 6, 24h) and analysed in biological quadruplicate (each of which represents a pool of two independent blood donors), in total representing 8 macrophage preparations from independent blood donors, on a custom-designed, focused microarray.

2012-03-28 | E-GEOD-19482 | biostudies-arrayexpress

Transcriptional responses of mouse BMM and TEPM to lipopolysaccharide (LPS)

Project description:Evolutionary change in gene expression is generally considered to be a major driver of phenotypic differences between species. We investigated innate immune diversification by analyzing inter-species differences in the transcriptional responses of primary human and mouse macrophages to the TLR4 agonist, LPS. Using a custom platform permitting cross-species interrogation coupled with deep sequencing of mRNA 5M-bM-^@M-^Y ends, we identified extensive divergence in LPS-regulated orthologous gene expression between humans and mice (24% of orthologs, http://www.macgate.qfab.org). Divergently regulated (DR) orthologs were enriched for genes encoding cellular M-bM-^@M-^\inputsM-bM-^@M-^] such as cell surface receptors (e.g. TLR6, IL-7RM-NM-1), and functional M-bM-^@M-^\outputsM-bM-^@M-^] such as inflammatory cytokines/chemokines (e.g. CCL20, CXCL13). Conversely, intracellular signaling components linking inputs to outputs were typically concordantly regulated. DR genes were associated with a large dynamic range of gene expression, and specific promoter architectural features (TATA box enrichment, CpG island depletion). Surprisingly, regulatory divergence was also associated with enhanced inter-species promoter conservation. Thus, the genes controlled by complex, highly conserved promoters that facilitate dynamic regulation are also the most susceptible to evolutionary change. Mouse macrophages (bone marrow-derived macrophages, BMM and thioglycollate-elicited peritoneal macrophages, TEPM) were stimulated with the TLR4 agonist, lipopolysaccharide, over a time course (0, 2, 6, 24h) and analysed in biological triplicate on a custom-designed, focused microarray.

2012-03-28 | E-GEOD-19490 | biostudies-arrayexpress

Transcriptome analysis of mesothelioma induced by intraperitoneal injections of asbestos in rats

Project description:Human malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. SM patients generally have poorer prognosis compared to EM patients. To identify potential genes accounting for the differential prognosis between these two subtypes, we compared the microarray gene expression profiles of rat SM and EM tissues induced by intraperitoneal injections of 3 types of asbestos (chrysotile,crocidolite and amosite). Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 28 microarrays (Whole Rat Genome Microarray) were used for screening purpose: The 2 arrays were used for knife-scraped peritoneal mesothelial cells, 2 arrays for cultured peritoneal mesothelial cells and 24 arrays for MM samples.

2014-06-04 | E-GEOD-48298 | biostudies-arrayexpress

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