Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of valproic acid on hematopoiesis: A functional profiling and cell phenotyping approach

ABSTRACT: Analysis of the effects of valproic acid (VPA) on chronic myelogenous leukemia K562 cells. This study attempts to elucidate the effects of VPA on cell homeostasis and hematopoietic differentiation pathways in this cell line. We used ten experimental conditions comparing valproic acid-treated and untreated cells at time points 2, 6, 10, 48 and 72 hrs respectively. Experiments were performed in three biological replicates including a dye swap (represented by replicate 3, for each timepoint).

ORGANISM(S): Homo sapiens

SUBMITTER: Marc Diederich

PROVIDER: E-GEOD-19939 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of heteronemin on gene expression profiles in chronic myelogenous K562 leukemia cells

Project description:Heteronemin is a sesterterpene first isolated from Hyrtios Erecta in 1976. In this study we decided to investigate the anti-cancer and anti-inflammatory potential of this marine natural compound at the transcriptomic level in chronic myelogenous K562 leukemia cells. Our results suggest that this sesterterpene has an impact on cell cycle, apoptosis, the MAP kinase signalling pathway and the NF-kappaB transcription factor. We used four experimental conditions : untreated cells, cells treated with heteronemin, cells treated with TNFalpha and cells co-treated with TNFalpha and heteronemin. Experiments were performed in three biological replicates including two technical replicates. Technical replicates were hybridized as dye-swaps. Dye-swap between replicates 1 and 2, 3 and 4, 5 and 6, respectively.

2009-10-14 | E-GEOD-16026 | biostudies-arrayexpress

human placenta-derived cell line (JEG-3): Control vs. valproic acid(VPA)-treated

Project description:Transcriptional profiling of human placenta-derived JEG-3 cell line comparing vehicle control with 7.38 mM of valproic acid(VPA)-treated JEG-3 cells for 48 hr. 7.38 mM valproic acid(VPA) induced the 30% inhibiotion of JEG-3 cell proliferation, G1 phase cell cycle arrest and the reduction of cell size. The Goal was to analyze the mechanism of valproic acid-induced adverse effects in placental cells. Two-condition experiment, JEG-3 cells vs. valproic acid(VPA)-treated JEG-3 cells. Biological replicates: 3 control replicates, 3 VPA-treated replicates.

2012-10-11 | E-GEOD-41441 | biostudies-arrayexpress

Gene expression profile of mouse ES cells treated with 1mM valproic acid for 8 hours

Project description:Histone deacetylase inhibitors (HDACi) cause hyperacetylation of bulk histones and H3K4 hypermethylation in a variety of cell types. They find clinical application as anti-epileptics and chemotherapeutic agents, but the pathways through which they alter cell physiology remain unclear. Surprisingly, changes in gene expression caused by HDACi are often limited in extent and can be positive or negative. Here we have explored the ability of the clinically important HDACi valproic acid (VPA) to alter gene expression in mouse embryonic stem (ES) cells. CCE/R mouse embryonic stem cells were treated with 1mM valproic acid for 8 hours. Four biological replicates were carried out. Treated cells were labelled with Cy5 and untreated controls with cy3 except in replicate 4 which was a dye-swap.

2013-03-29 | E-GEOD-45610 | biostudies-arrayexpress

Saccharomyces cerevisiae mutant strain with R1158 strain background: Fold change after doxycycline treatment

Project description:To understand the extent that Heat shock protein 90 (Hsp90) regulated its target proteins at the transcription level, transcriptomic change was profiled in yeast cells upon Hsp90 compromising. We genetically modified the R1158 strain (resulting genotype of mutant strain: TETp-HSC82 hsp82Δ arg4Δ lys5Δ car2Δ::URA3) and then reduced the Hsp90 amount with doxycycline treatment. Fold change of mRNA from untreated to treated cells indicated the transcriptomic change. Totally, we identified 1104 genes mis-regulated with a fold change of no less than 1.5 (P <0.05) upon Hsp90 compromising. Two-condition experiment, treated vs. untreated cells. Biological duplicates, independently grown and harvested. Technical triplicates for RNA isolation.

2014-03-26 | E-GEOD-56186 | biostudies-arrayexpress

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

Project description:Although Lgr5+ intestinal stem cells have been expanded in vitro as organoids, homogeneous culture of these cells has not been possible so far. Here we show that two small molecules, CHIR99021 and valproic acid, synergistically maintain self-renewal of mouse Lgr5+ intestinal stem cells, resulting in nearly homogeneous cultures. The colony-forming efficiency of cells from these cultures is ~100-fold greater than that of cells cultured in the absence of CHIR99021 and valproic acid, and multilineage differentiation ability is preserved. We made use of these homogeneous cultures to identify conditions employing simultaneous modulation of Wnt and Notch signaling to direct lineage differentiation into mature enterocytes, goblet cells and Paneth cells. Expansion in these culture conditions may be feasible for Lgr5+ cells from the mouse stomach and colon and from the human small intestine. These methods provide new tools for the study and application of multiple intestinal epithelial cell types. Total RNA was isolated from two independently established wild-type mouse small intestinal organoid lines after culture for 6 days in control condition or in the presence of CHIR99021, Valproic Acid (VPA) or both compounds. cRNA was labeled with Cy5 and hybridized against Cy3 labeled cRNA from control organoids (as an internal reference) on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F), resulting in eight individual arrays.

2013-11-22 | E-GEOD-51539 | biostudies-arrayexpress

LNCaP cells: shRNA library with bicalutamide

Project description:Short hairpin RNA library-based functional screening identified ribosomal protein L31 that modulates prostate cancer cell growth Vehicle vs. bicalutamide treated LNCaP cells infected with lentiviral shRNA library. Biological replicates: 2 vehicle treatments, 2 bicalutamide treatments.

2015-05-15 | E-GEOD-60382 | biostudies-arrayexpress

Transcriptome changes for Hirschfeldia incana in response to lead exposure

Project description:Experiments were achieved on Hirschfeldia incana, a Brassicaceae collected from metalliferous mine spoils as a Pb accumulator plant. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old H. incana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 100 M-BM-5M Pb(NO3)2. Two-condition experiment, lead treated vs. untreated. Biological replicates: 3

2015-01-28 | E-GEOD-65332 | biostudies-arrayexpress

Transcriptome changes for Arabidopsis thaliana in response to lead exposure

Project description:Experiments were achieved on Arabidopsis thaliana. Transcriptional profiling of roots and shoots from plants treated with lead were compared to plants treated in similar conditions without lead. Four weeks old A. thaliana seedlings were treated in hydroponic cultures with Pb during 3 days, by adding or not 40 M-BM-5M Pb(NO3)2. Two-condition experiment, lead treated vs. untreated. Biological replicates: 3

2015-01-28 | E-GEOD-65333 | biostudies-arrayexpress

Transcriptome changes in response to lead exposure

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-28 | E-GEOD-65334 | biostudies-arrayexpress

IFN-alpha- and IFN-gamma-regulated transcription in MEFs derived from wild type mice or littermates expressing STAT1F77A

Project description:Transcriptional profiling of mouse primary embryonic fibroblasts (MEFs) from wild type (WT) and knockin littermates expressing STAT1F77A (KI). For both genotypes, untreated control cells were compared to cells treated with IFN-alpha or IFN-gamma. Two condition experiments; untreated versus IFN treated

2014-01-12 | E-GEOD-49441 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data