Expression analysis of plants with altered GEM mRNA levels, with and without ABA treatment (2 hours).
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE45038 | GEO | 2019/07/01
REPOSITORIES: GEO
Similar Datasets
Project description:Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA.
2011-02-09 | GSE27036 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response
2008-11-19 | GSE9646 | GEO
Project description:Blocking ABA-signaling and ABA-treatment; ABA treatment dependence on VND transcription factors
| PRJNA716326 | ENA
Project description:Background: Histone deacetylase (HDAC) is strongly associated with epigenetic regulation and carcinogenesis, and its inhibitors induce the differentiation or apoptosis of cancer cells. Valproic acid (VPA) is one of the clinically available HDAC inhibitors. We investigated the anticancer effects of VPA in combination with gemcitabine (GEM) in cholangiocarcinoma cell line, and explored the mechanisms of the anticancer effects using microarray analysis. Methods: A human cholangiocarcinoma cell line (HuCCT1) was used. The anticancer effects of VPA, or gemcitabine (GEM), and the effects of VPA combined with GEM, were studied by cell proliferation assay. The microarray analysis was performed, the genes were picked up using Gene Spring GX11.5, Ingenuity Pathways Analysis (IPA) was performed, and then the gene-expression was determined by RT-PCR. Results: GEM (5nM) and VPA (0.5mM) reduced by 23%, which significantly augmented the anticancer effect of GEM alone or VPA alone (P<0.01). Using the microarray analysis, forty-three genes were identified with the comparison between GEM group and GEM plus VPA combination group. The interactions were shown between genes of the “Cellular Development” relevant to the differentiation of cancer cell using IPA. Total RNA was isolated from both the stimulated and unstimulated cells (HuCCT-1) using RNeasy Mini kit (Qiagen, Valencia, CA). Relative purity was examined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA expression was analyzed using GeneChip○R Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA, USA), containing 28,869 oligonucleotide probes for known and unknown genes. First standard cDNA was synthesized from 300 ng of total RNA by using GeneChip○R Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) according to the manufacturer’s instructions. 10 μg of cRNA were input into the second-cycle cDNA reaction. cDNA was fragmented and end-labeled with the GeneChip○R WT Terminal Labeling Kit (Affymetrix). Approximately 5.5μg of fragmented and labeled DNA target was hybridized to the Affymetrix GeneChip○R Human Gene 1.0 ST Array at 45°C for 17h on a GeneChip○R Hybridization Oven 640 (Affymetrix) according to the manufacturer’s recommendation. Hybridized arrays were washed and stained on a GeneChip○R Fluidics Station 450 and scanned on a GeneChip○R Scanner 3000 7G (Affymetrix), and then generated CEL files for each array. The microarray data was normalized by GeneSpring GX 11.5 software (Agilent). The cut-off value was set at 0.5 to 2.0 for the ratio (more than 2.0: up-regulation, 0.5-2.0: no change, less than 0.5: down-regulation). Gene Ontology (GO) was analyzed using GeneSpring GX 11.5 software (Agilent), and p-value < 0.05 was used for significance. Then we used Ingenuity Pathway Analysis (IPA) 8.7 (http://www.ingenuity.com) to determine the functional pathways associated with the set of differentially expressed genes between genotypes. IPA utilizes the knowledge in the literature about biological interactions among genes and proteins.
2011-02-09 | E-GEOD-27036 | biostudies-arrayexpress
Project description:Microarray experiments were performed using Arabidopsis wild type plants (Col-0) and srk2cf double knockout mutants to investigate functions of two osmotic stress-activated protein kinases, SRK2C and SRK2F. Transcription profiles of wild type and mutants were compared under abscisic acid (ABA) treatment for 0, 1 and 4 h.
2009-10-15 | E-MEXP-2378 | biostudies-arrayexpress
Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to ABA treatment, at two time points, each including triplicated measurements Keywords: ABA response
2009-04-29 | GSE10328 | GEO
Project description:RNA sequencing was peformed on RNA isolated from melanomas collected from TN GEM models upon reach exclusion criteria.
2022-04-30 | GSE197841 | GEO
Project description:The aim of this experiment is to understand the impact of overexpression of ERD15 on the transcriptome of Arabidopsis thaliana. ERD15 was isolated from a screen for genes rapidly induced after pathogen treatment from Arabidopsis. This gene was originally found as early responsive to drought (Kiyosue et al., 1994, Plant Physiol 106, 1707). ABA is central phytohormone in drought response, but increasing information is pointing to its significant role in pathogen responses as well. We are interested to see the effect of this hormone on plants overexpressing ERD15 compared to control plants. The samples (rosette leaves)will be harvested from 3-week old soil grown plants 90 min after spraying with 100 micromolar ABA. Comparison will be made with non-treated plant samples. Experimenter name = Elina Helenius Experimenter phone = +358 9 191 59085 Experimenter fax = +358 9 191 59079 Experimenter institute = University of Helsinki Experimenter address = Viikinkaari 5 D Experimenter address = P.O.Box 56 Experimenter address = Helsinki Experimenter zip/postal_code = 00014 Experimenter country = Finland Keywords: compound_treatment_design
2006-08-15 | GSE5521 | GEO
Project description:We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome under drought, cold, high-salinity and ABA treatment conditions and idenfied many stress- or ABA- responsive putative functional RNAs and fully-overlapping sense-antisense transcripts in Arabidopsis genome. Keywords: stress response Two-week-old Arabidopsis plants grown on the agar plates were subjected to the stress- or ABA- treatments. The total RNA was prepared from the treated- and untreated- plants, and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.
2008-11-19 | E-GEOD-9646 | biostudies-arrayexpress
Project description:Transcriptional reprogramming plays a key role in drought stress responses, preceding the onset of morphological and physiological adaptations. The best characterised signal regulating gene expression in response to drought is the phytohormone abscisic acid (ABA). ABA-regulated gene expression, biosynthesis and signalling are highly organised in a diurnal cycle, so that ABA-regulated physiological traits occur at the appropriate time of the day. The mechanisms that underpin such diel oscillations in ABA signals are poorly characterised. Here we uncover GIGANTEA (GI) as a key gate keeper of ABA-regulated transcriptional and physiological responses. Time-resolved RNAseq under different irrigation scenarios indicate that gi mutants produce an exaggerated ABA response at midday, despite accumulating wild-type levels ABA. The direct comparison with ABA-deficient mutants confirms the role of GI in controlling ABA-regulated genes and enabled us to distinguish a phase of high ABA sensitivity at dawn, characterized by low GI accumulation.
2022-07-11 | GSE181083 | GEO