Expression data from differentiating murine embryonic stem cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE54242 | GEO | 2015/05/21
SECONDARY ACCESSION(S): PRJNA236079
REPOSITORIES: GEO
Similar Datasets
Project description:Various substances have been reported to enhance the cardiac differentiation of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Ascorbic Acid had a cardiogenic effect in mESC CGR8 cell line. Transcriptome of AA-treated CGR8 ESCs did not reveal any significant changes in gene expression as compared to untreated cells. We performed a global gene expression analysis to better understand the mechanism of Ascorbic acid-induced cardiac differentiation. Differentiating murine embryonic stem cells from CGR cell line were selected at stages of Day 0 (undifferentiated cells), Day 2, Day 3 and Day 5 of differentiation for RNA extraction and hybridization on Affymetrix microarray chip. Samples were collected in 3 biological replicate and were either treated with Ascorbic acid or nontreated (control group). Only those samples were processed for further analysis in which we were able to confirm that AA significantly enhanced cardiac differentiation efficiency at later stages (day 8 and 12) of differentiation by assessing the number of beating EBs in control and AA-treated groups. Cardiac efficiency was evaluated later on this study. But samples that were analyzed by microarray analysis was limited till Day 5. We did not perform whole genome study for these later days of differentiation ( day 8 or 12).
2015-05-21 | E-GEOD-54242 | biostudies-arrayexpress
Project description:Reprogramming intermediates (pre-iPSCs) were subjected to control DMSO, ascorbic acid (AA), 2i ( MAP kinase inhibitor + GSKinhibitor) or AA+2i conditions to assess conversion to the iinduced pluripotent stem cell state (iPSC) after 10days.
2015-01-13 | GSE58836 | GEO
Project description:Background: Clear guidelines for therapy of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) are missing due to the lack of randomized double-blind controlled clinical trials. Moderate yet similar clinical benefit has been demonstrated for IFN-a monotherapy and high-dose ascorbic acid (AA) monotherapy in open clinical trials. However, there is no clear evidence to support the value of one of these specific treatment approaches, due to the lack of in vivo and in vitro studies exploring and comparing the effects of high-dose AA and IFN-a treatment in the context of HAM/TSP. Principal Findings: Based on flow cytometry and thymidine incorporation, we demonstrated for the first time that high-dose AA displays superior antiproliferative and immunomodulatory effects over IFN-a in HAM/TSP PBMCs ex vivo. In addition, high-dose AA induces cell death in HTLV-1-infected T-cell lines in vitro. Microarray combined with Ingenuity Pathway Analysis revealed AA-induced modulation of genes associated with cell death and cell cycle. Conclusions: In comparison with IFN-a, high-dose AA is preferred as anti-HTLV-1 treatment in vitro, due to its superior cell death-inducing, antiproliferative and immunomodulatory effects. Considering the lack of treatment options, the mild in vivo side effects and the low cost price, high-dose AA should be further explored for its therapeutic potential in HAM/TSP treatment. In total, 15 samples were analyzed. One microarray experiment was performed, including triplicate samples for each treatment condition (untreated, IFN-a, 10 µg/ml ascorbic acid, 50 µg/ml ascorbic acid, 100 µg/ml ascorbic acid). Triplicate samples were obtained from three separate RNA experiments.
2012-06-13 | E-GEOD-34572 | biostudies-arrayexpress
Project description:Rationale: Cardiac development is a complex process that results in the first integrated, multi-lineage embryonic tissue. Imperfect developmental progression leads to congenital heart disease, the most common birth defect with developmental corruption affecting more than 1% of all live births. Interrogation of individual genes has provided the backbone for cardiac developmental biology, yet a comprehensive transcriptome derived from natural cardiogenesis is required to establish an unbiased roadmap to gauge innate developmental milestones necessary for stem cell-based differentiation and in vitro disease modeling. Objective: Establish a contextual expression database of spatial-temporal cardiac structures, and validate a predictive tool to diagnose and predict cardiogenic outcomes from individual pluripotent stem cell lines. Methods and Results: Stage-specific cardiac structures were dissected from eight distinctive embryonic time points to produce a genome-wide expressome analysis across the spectrum of early to late cardiogenesis. Hierarchical clustering of the time course dataset demonstrated discrete gene expression profiles during natural embryonic development. In reference to the native cardiogenic expression roadmap, disruptive iPSC-derived cardiac expression profiles were revealed from pro-cardiogenic 3-factor (SOX2, OCT4, KLF4) compared to non-cardiogenic 4-factor (addition of c-MYC) reprogramming regimens upon stage-specific differentiation. Expression of cardiac-related genes from 3F-iPSC differentiated in vitro at day 0, 5, and 11 recapitulated expression of natural embryos at days 0, E7.5-E8.5, and E14.5-E18.5, respectively. In contrast, 4F-iPSC demonstrated variable gastrulation gene expression profiles beginning at day 5 of differentiation. Differential gene expression within the pluripotent ground state between the archetypical high cardiogenic potential of embryonic stem cells recapitulated in 3F-iPSC vs. the low cardiogenic potential of 4F-iPSC revealed 23 distinguishing candidate genes. Upon subsequent differentiation, cell line-specific gene expression differences were magnified to 399 genes at day 5 and 726 genes at day 11. A confirmed panel of 20 genes, differentially expressed between high and low cardiogenic cell lines, was transformed into a predictive score that was sufficient to correctly rank independent iPSC lines according to cardiogenic potential. Conclusions: Transcriptome analysis attuned to the embryonic developing heart provides a robust platform to probe coordinated cardiac specification and maturation from stem cell-based cardiogenesis model systems. Based on this genome-wide expressome roadmap, a panel of pre-cardiac genes was extracted that allowed differential prognosis of cardiogenic competency from individual reprogrammed cell lines at the pluripotent state. The overall experimental design includes 3 time points (Day0, Day5, Day11) and 3 different stem cell lines: R1 embryonic stem cells (ESCs), H9 induced pluripotent stem cells (H9-iPSCs) generated/reprogrammed by 3 transcription factors (called 3F-iPSCs), and 19BL induced pluripotent stem cells (19BL-iPSCs) generated/reprogrammed by 4 transcription factors (called 4F-iPSC). At each time point, each cell line has 3 biological replicates. In total, there are 27 samples. R1-embryonic stem cells (R1-ESCs): Day0 undifferentiated ESCs - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 3F-iPSC (H9 iPSCs): Day 0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates. 4F-iPSC (19BL-iPSCs): Day0 undifferentiated - 3 biological replicates, Differentiated for 5 days (Day5) - 3 biological replicates, Differentiated for 11 days (Day11) - 3 biological replicates.
2013-09-23 | E-GEOD-43197 | biostudies-arrayexpress
Project description:We report a time course of RNA-seq data from wild-type embryonic stem cells and embryonic stem cells in which the cardiogenic transcription factors ZNF503, ZEB2 and NKX2-5 are depleted with shRNAs differentiating along the cardiac lineage. Biological replicates of RNA-seq data from embryonic stem cells differentiating along the cardiac lineage.
2015-06-06 | E-GEOD-69618 | biostudies-arrayexpress
Project description:Ascorbic acid (AA) is known to play a vital role in plant growth and detoxification of reactive oxygen species, however little is known about the significance of AA oxidation in plant defence against pathogens. • The role of ascorbate oxidation in rice defence against root-knot nematodes, Meloidogyne graminicola, was tested with application of AA, ascorbate oxidase (AO), dehydroascorbic acid (DHA), biosynthesis inhibitors and use of mutants. Transcriptome analysis was done on AO treated plants, and hormone measurements were executed to confirm the results. Biochemical analyses were used to study oxidative stress markers, including accumulation of H2O2, , malondialdehyde and AA/DHA.
2020-01-22 | GSE125427 | GEO
Project description:Previous preclinical study has shown that high levels of ascorbic acid (AA) possesses the ability to kill human colorectal cancer cells and high expression of GLUT3 will augment the efficacy of AA. To date, no previous studies have investigated the therapeutic role of AA in peritoneal metastatic colorectal cancer with high expression of GLUT3. This protocol is a randomized controlled study of AA infusions combined with FOLFOXIRI +/- bevacizumab versus treatment with FOLFOXIRI +/- bevacizumab alone in peritoneal metastatic colorectal cancer patients with high expression of GLUT3.
| 2349088 | ecrin-mdr-crc
Project description:Preclinical study has shown that human colorectal cancer cells harboring KRAS or BRAF mutations are selectively killed by high levels of ascorbic acid (AA). High dose of AA aslo impairs tumor growth in Apc/KRASG12D mutant mice. Previous phase Ⅰ studies have found that high dose iv AA is well tolerated in cancer patients.This protocol is a phase Ⅲ study of AA infusions combined with treatment with FOLFOX +/- bevacizumab versus treatment with FOLFOX +/- bevacizumab alone as first-line therapy in patients with recurrent or advanced colorectal cancer.
| 2230288 | ecrin-mdr-crc
Project description:We report a time course of RNA-seq data from wild-type embryonic stem cells and embryonic stem cells in which the cardiogenic transcription factors ZNF503, ZEB2 and NKX2-5 are depleted with shRNAs differentiating along the cardiac lineage.
2015-06-06 | GSE69618 | GEO
Project description:Aristolochic acid (AA) is a major ingredient in several Chinese herbs that exhibits a wide range of pharmacological effects. Recently, clinical reports and experimental studies have demonstrated that AA causes renal toxicities, acute renal failure and interstitial fibrosis.However, the molecular mechanism underlying AA nephrotoxicity is not yet fully understood. Embryonic stem cells (ESCs) are pluripotent cells isolated from early embryos, which have highly undifferentiated potential and are capable of differentiating into all kinds of body tissues and organs. It has been reported that ESCs are sensitive to drug stimulation, and thus may serve as important tools for in vitro assessment of drug toxicity. We aimed to identify accurate biomarkers of AA-induced renal toxicity on ESCs. Genomics analysis was performed to screen the changes in gene expression levels of ESCs following treatment with AA, in order to determine the potential biological processes in which AA induces renal toxicity.
2020-11-27 | GSE162195 | GEO