Induction of germline-competent pluripotent stem cells from mouse fibroblasts has been achieved by the ectopic expression of four genes (Oct3/4, Sox2, c-Myc and Klf4). If this method can be applied to humans for the generation of personalized human pluripotent stem cells, it would greatly facilitate the therapeutic application of stem cells by avoiding the problem of immune rejection by the recipient associated with allograft transplants. Here we show that the ectopic expression of the same four genes in human neonatal skin derived cells is sufficient to induce pluripotent stem cells indistinguishable from human embryonic stem cells in morphology, gene expression, DNA methylation, teratoma formation and long term self-renewal ability. Extensive analysis of colonies generated by ectopic expression of these four genes indicates the presence of considerable heterogeneity in the induced colonies. These results provide a new finding to generate human induced pluripotent stem cells from postnatal somatic tissues.
Heterogeneity of pluripotent marker gene expression in colonies generated in human iPS cell induction culture.
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View SamplesMice with MUTYH-null allele (Mutyh+/-, Mutyh-/-) were fed a high-fat/high-cholesterol (HFHC) diet or HFHC + high iron diet. The incidence of liver tumors and histological features of the liver were compared.
MUTYH is associated with hepatocarcinogenesis in a non-alcoholic steatohepatitis mouse model.
Specimen part, Disease, Treatment
View SamplesPlant hormones interact with each other and regulate gene expression to control plant growth and development. To understand the complex network, accumulation of comprehensive and integrative data of gene expression and hormone concentration is important. Using microarray, global gene expression profile was analyzed to compare with plant hormone concentration in 14 parts of rice at reproductive stage.
UniVIO: a multiple omics database with hormonome and transcriptome data from rice.
No sample metadata fields
View SamplesThe unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors.
Chemical genomics identifies the unfolded protein response as a target for selective cancer cell killing during glucose deprivation.
No sample metadata fields
View SamplesNitrogen (N) is a key nutrient that is often the limiting factor in plant growth. However, the molecular mechanisms underlying transcriptional regulation of N-starvation-responses remain largely unknown.
A NIGT1-centred transcriptional cascade regulates nitrate signalling and incorporates phosphorus starvation signals in Arabidopsis.
Specimen part
View SamplesDuring a binary cell fate decision, a progeny silences the gene expression program associated with the alternative fate. Helper versus cytotoxic lineage decision in the thymus has been studied as a model for gene silencing of alternative lineage genes, including Cd4. While RUNX3 is required for the initiation of Cd4 silencing, it remains unknown how silenced states of Cd4 and other helper lineage genes are maintained. We show that the histone methyltransferase G9a is necessary for heritable silencing of Cd4 and other helper lineage genes in CD8 T cells. Despite normal Cd4 downregulation during the development, G9a-deficient CD8 T cells fail to maintain silencing of helper lineage genes when they repeatedly divide under non-inflammatory conditions. However, Cd4 depression is prevented during division driven by elevated TCR signaling and an inflammatory cytokine signaling. These results reveal the requirement for G9a in silencing of helper lineage genes in CD8 T cells and also suggest that CD8 T cells employ an alternative mechanism to maintain their cellular identity during immune responses. Overall design: RNA-sequencing on CD4+CD8+ G9a KO, CD4–CD8+ G9a KO, and CD4–CD8+ G9a WT T cells after 4 weeks of proliferation in a lymphopenic environment. ChIP-sequencing on H3K9me3 IP''ed from Ehmt2+/+ and Ehmt2-/- CD8+ T cells cultured in vitro with antibodies to CD3 and CD28
Cutting Edge: The Histone Methyltransferase G9a Is Required for Silencing of Helper T Lineage-Associated Genes in Proliferating CD8 T Cells.
Specimen part, Cell line, Subject
View SamplesGenes related to sleep and wakefulness were evaluated by RNA microarray in patients, including CKD,HD patients and control subjects.
Messenger RNA expression profile of sleep-related genes in peripheral blood cells in patients with chronic kidney disease.
Sex, Specimen part
View SamplesInhibiting the unfolded protein response (UPR) can be a therapeutic approach, especially for targeting the tumor microenvironment. We found that compound C (also known as dorsomorphin) prevented the UPR and exerted enhanced cytotoxicity during glucose deprivation. The UPR-inhibiting activity of compound C was not associated with either AMPK or BMP signaling inhibition.
Compound C prevents the unfolded protein response during glucose deprivation through a mechanism independent of AMPK and BMP signaling.
Specimen part, Cell line
View SamplesCancer cells consume large amounts of glucose because of their specific metabolic pathway. However, cancer cells exist in tumor tissue where glucose is insufficient. To survive, cancer cells likely have the mechanism to elude their glucose addiction. Here we show that functional mitochondria are essential if cancer cells are to avoid glucose addiction.
Mitochondria regulate the unfolded protein response leading to cancer cell survival under glucose deprivation conditions.
Disease, Cell line, Time
View SamplesWe examined the effect of quercetin on the gene expression and function of epididymal adipose tissue (EAT) in Western diet-induced obese mice. Quercetin suppressed the increase in the number of macrophages and the decrease in the ratio of CD4+ to CD8+ T cells in EAT, and the elevation of plasma leptin and TNF levels in mice fed the Western diet. Comprehensive gene expression analysis revealed that quercetin suppressed gene expression associated with the accumulation and activation of immune cells, including macrophages and lymphocytes in EAT. It also improved the expression of the oxidative stress-sensitive transcription factor NFB, NADPH oxidases, and antioxidant enzymes. Quercetin markedly increased gene expression associated with mitochondrial oxidative phosphorylation and mitochondrial DNA Quercetin most likely universally suppresses the accumulation and activation of immune cells, including anti-inflammatory cells, whereas it specifically increased gene expression associated with mitochondrial oxidative phosphorylation. Suppression of oxidative stress and NFB activity likely contributed to the prevention of the accumulation and activation of immune cells and resulting chronic inflammation.
Quercetin suppresses immune cell accumulation and improves mitochondrial gene expression in adipose tissue of diet-induced obese mice.
Sex, Specimen part
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