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EScell data, composed of normalized log ratio of the differentiated compared to the undifferentiated at 5 points

ABSTRACT: The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. We analyzed the gene expression microarray data, composed of the fluorescent signal intensity ratio, of the differentiated (Cy5 channel; red) compared to the undifferentiated (Cy3 channel; green) at 5 points in time: we started with a treatment with ATRA (Start), 2 days for neuronal induction (2 after), 0 day after the neuronal induction (0 day), 2 days after the neuronal induction (2 days), 7 days after the neuronal induction (7 days).

ORGANISM(S): Mus musculus

SUBMITTER: Jung_Hee Shim

PROVIDER: E-GEOD-4687 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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EScell data, composed of normalized log ratio of the differentiated compared to the undifferentiated at 5 points

Project description:The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. Keywords: time course, embryonic stem cell

2006-05-09 | GSE4687 | GEO

Log-ratio lasso: Scalable, sparse estimation for log-ratio models.

Project description:Positive-valued signal data is common in the biological and medical sciences, due to the prevalence of mass spectrometry other imaging techniques. With such data, only the relative intensities of the raw measurements are meaningful. It is desirable to consider models consisting of the log-ratios of all pairs of the raw features, since log-ratios are the simplest meaningful derived features. In this case, however, the dimensionality of the predictor space becomes large, and computationally efficient estimation procedures are required. In this work, we introduce an embedding of the log-ratio parameter space into a space of much lower dimension and use this representation to develop an efficient penalized fitting procedure. This procedure serves as the foundation for a two-step fitting procedure that combines a convex filtering step with a second non-convex pruning step to yield highly sparse solutions. On a cancer proteomics data set, the proposed method fits a highly sparse model consisting of features of known biological relevance while greatly improving upon the predictive accuracy of less interpretable methods.

| S-EPMC9470385 | biostudies-literature

RNA sequencing of undifferentiated and differentiated SH SY5Y cells

Project description:DNA topoisomerase IIB has an important role in ligand mediated transcriptional regulation of gene expression. SH-SY5Y is a neuroblastoma cell line that can be induced to differentiate into neuronal-like cells in response to retinoic acid. In this study TOP2B has been knocked out using crispr-cas9 to determine the role of TOP2B in the transcriptional response to retinoic acid. RNA was prepared from untreated wild type and TOP2B null SH-SY5Y cells and from cells exposed to 10 uM All Trans Retinoic Acid (ATRA) for 24 hours.

2022-06-28 | GSE142383 | GEO

Expression Profiling of HL-60 Cells Stimulated by ATRA and DMSO

Project description:Stimulation of HL60 progenitor cells with either DMSO (1.25% v/v) or atRA (10E-07M) resulted in their differentiation into neutrophils within six days. Gene expression profiles across 12 600 genes were measured for the differentiation processes induced by DMSO and atRA at 0, 2, 4, 8, 12, and 18 h and daily thereafter until day 7 using oligonucleotide DNA microarrays. Keywords: time course, differentiation, cell fate transitions

2009-01-22 | GSE14500 | GEO

Expression data from Verbenalin-treated human amnion epithelial cells (hAECs)

Project description:Gene expression profiling reveals a potential role of Verbenalin in neural induction and neuronal differentiation of hAECs. hAECs were isolated from discarded term placenta and were treated with 20 μM verbenalin for seven days. Microarray gene expression profiling was conducted for biological replicates of RA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7).

2019-09-09 | GSE137061 | GEO

Long Intergenic Non-Coding RNA HOTAIRM1 Regulates Cell Cycle Progression During Myeloid Maturation in NB4 Promyelocytic Leukemia Cells

Project description:HOTAIRM1 is a long intergenic non-coding RNA located in the human HOXA gene cluster, with gene expression highly specific for maturing myeloid cells, particularly during all-trans retinoic acid (ATRA) induction of granolopoiesis in NB4, a human t(15;17) acute promyelocytic leukemia (APL) cell line. We sought to assess the impact of HOTAIR knockdown on the global programme of gene expression underlying the granulocytic maturing process in NB4 cells. The knockdown of HOTAIRM1 resulted in a less differentiated expression profile in the NB4 cells after 4 days of ATRA-induced granulocytic differentiation, with retained expression of many otherwise ATRA-suppressed cell cycle and DNA replication genes, as well as abated induction of cell surface leukocyte activation and defense response genes.

2014-04-30 | GSE49516 | GEO

Elevated International Normalized Ratio Is Associated With Ruptured Aneurysms.

Project description:Background and Purpose- The effects of anticoagulation therapy and elevated international normalized ratio (INR) values on the risk of aneurysmal subarachnoid hemorrhage are unknown. We aimed to investigate the association between anticoagulation therapy, elevated INR values, and rupture of intracranial aneurysms. Methods- We conducted a case-control study of 4696 patients with 6403 intracranial aneurysms, including 1198 prospective patients, diagnosed at the Massachusetts General Hospital and the Brigham and Women's Hospital between 1990 and 2016 who were on no anticoagulant therapy or on warfarin for anticoagulation. Patients were divided into ruptured and nonruptured groups. Univariable and multivariable logistic regression analyses were performed to evaluate the association of anticoagulation therapy, INR values, and presentation with a ruptured intracranial aneurysm, taking into account the interaction between anticoagulant use and INR. Inverse probability weighting using propensity scores was used to minimize differences in baseline demographics characteristics. The marginal effects of anticoagulant use on rupture risk stratified by INR values were calculated. Results- In unweighted and weighted multivariable analyses, elevated INR values were significantly associated with rupture status among patients who were not anticoagulated (unweighted odds ratio, 22.78; 95% CI, 10.85-47.81 and weighted odds ratio, 28.16; 95% CI, 12.44-63.77). In anticoagulated patients, warfarin use interacts significantly with INR when INR ≥1.2 by decreasing the effects of INR on rupture risk. Conclusions- INR elevation is associated with intracranial aneurysm rupture, but the effects may be moderated by warfarin. INR values should, therefore, be taken into consideration when counseling patients with intracranial aneurysms.

| S-EPMC6205738 | biostudies-literature

International normalized ratio and activated partial thromboplastin time testing.

Project description: Not available

| S-EPMC9435534 | biostudies-literature

Expression data from rosmarinic acid-treated human amnion epithelial cells (hAECs)

Project description:Gene expression profiling reveals a potential role of rosmarinic acid in neural induction and neuronal differentiation of hAECs. hAECs were isolated from discarded term placenta and were treated with 20 μM RA for seven days. Microarray gene expression profiling was conducted for biological replicates of RA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7).

2019-06-26 | GSE133277 | GEO

A method of back-calculating the log odds ratio and standard error of the log odds ratio from the reported group-level risk of disease.

Project description:In clinical trials and observational studies, the effect of an intervention or exposure can be reported as an absolute or relative comparative measure such as risk difference, odds ratio or risk ratio, or at the group level with the estimated risk of disease in each group. For meta-analysis of results with covariate adjustment, the log of the odds ratio (log odds ratio), with its standard error, is a commonly used measure of effect. However, extracting the adjusted log odds ratio from the reported estimates of disease risk in each group is not straightforward. Here, we propose a method to transform the adjusted probability of the event in each group to the log of the odds ratio and obtain the appropriate (approximate) standard error, which can then be used in a meta-analysis. We also use example data to compare our method with two other methods and show that our method is superior in calculating the standard error of the log odds ratio.

| S-EPMC7053742 | biostudies-literature

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