WT and php mutants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE13913 | GEO | 2010/04/01
SECONDARY ACCESSION(S): PRJNA110333
REPOSITORIES: GEO
Similar Datasets
Project description:Comparison of gene expression profiles of mouse bone marrow nucleated cells. All comparisons are made between biological replicates (different mice) derived from animals carrying the Type A cytoplasmic Nucleophosmin mutation (Npm1c) found in human Acute Myeloid Leukaemia. Mice were culled 8 weeks after induction of the conditional Npm1c allele with Mx1-Cre. Whole bone marrow (BM, n=20: 11xNpm1c & 9xWildType) or antibody purified cell fractions (Lin minus, n=6: 4xNpm1c & 2xWildType; B220+, n=5: 3xNpm1c & 2xWildType and Gr1+/Mac1+, n=6: 4xNpm1c & 2xWildType) were studied. Files ("samples") include data from all samples in each comparison.<br>Global profiling was done using Illumina mouse-6 expression beadchip version 2. Data were quantile normalised and analysed using the bioconductor (http://www.bioconductor.org/), lumi (http://www.bioconductor.org/packages/2.0/bioc/html/lumi.html ) and limma packages, then p-value adjusted for multiple testing.
2011-03-15 | E-MEXP-3113 | biostudies-arrayexpress
Project description:DCA (3,5-Dichloroanthranilic acid) is a newly identified synthetic defense elicitor. To perform a comparative analysis of defense responses triggered by DCA and the structurally related defense inducer INA (2,6-Dichloroisonicotinic acid) Affymetrix chip experiments were performed with Arabidopsis thaliana seedlings treated with one of these two compounds. Experiment Overall Design: Arabidopsis thaliana plants (accession Col-0) were grown on soil in a semi-sterile growth chamber under fluorescent lights (14 hours light, 10 hours dark, 21 centi grades, 100 Einstein/m2/s). Wild type Col-0 plants and the npr1-3 mutant were used in this study. Aerial tissues of 2 week old soil grown Arabidopsis seedlings were sprayed with 100uM 3,5-Dichloroanthranilic acid (DCA), or 100uM 2,6-Dichloroisonicotinic acid (INA) or mock solution and harvested 48h or 6 days after the treatment. Final DMSO concentrations never exceeded 0.002%. Mock treatments were application of 0.002% DMSO in water. For harvesting the aerial plant parts were shock-frozen in liquid nitrogen. Total RNA was isolated from seedlings using TRIZOL (Invitrogen) follwing the manufacturerâ??s instructions. RNA was processed and hybridized to Affymetrix Arabidopsis ATH1 genome array GeneChip following manufacturerâ??s instructions (Affymetrix) by the University of California, Riverside Core Instrument Facility. Three independent biological replicates were performed for each treatment.
2009-03-28 | E-GEOD-13833 | biostudies-arrayexpress
Project description:While the close relationship between BRs and auxin has been widely reported, the molecular mechanism for combinatorial control of shared target genes has remained elusive. In this work, we demonstrate that BRs synergistically increase seedling sensitivity to auxin and show that combined treatment with both hormones can increase the magnitude and duration of gene expression. arf2 mutants are less sensitive to changes in endogenous BR levels, while a large number of genes affected in an arf2 background are returned to near wild-type levels by altering BR biosynthesis. Together, these data suggest a model where BIN2 increases expression of auxin-induced genes by directly inactivating repressor ARFs, leading to synergistic increases in transcription. Experiment Overall Design: Total RNA was extracted from 4-day-old, etiolated Arabidopsis seedlings grown on 0.5 µM BRZ or mock treatments and used to probe ATH1 microarrays (Affymetrix), according to manufacturerâ??s protocols. There are three independent biological replicates for each genotype and treatment, except for arf2 mutants with BRZ where only two arrays passed quality control. We performed standard Affymetrix quality-control procedures using the BioConductor packages simpleaffy. Expression was normalized and estimated using the gcRMA package of BioConductor.
2008-10-20 | E-GEOD-11216 | biostudies-arrayexpress
Project description:Plants were grown in a mix (2:1) of soil and vermiculite in individual pots and cultivated in a growth chamber with 60-70% relative humidity and a day/night cycle (16hr-23°C/8h-20°C) at around 110 mol.m-2.s-1. For the microarray and metabolomic experiments, leaves of med18, med25, and WT were collected at the bolting time of WT. The experiments were repeated at least 3 times.Leaves of plants (mutants and WT) grown in LD conditions were collected, frozen and stored at –80°C until extraction. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen Nordic, Sollentuna, Sweden). For each sample the DNase treatment was performed during the extraction according to the Qiagen protocol with RNase-free DNase I (Qiagen) to eliminate genomic DNA contamination. ATH1 Affymetrix GeneChip microarrays were performed using 10 μg of total RNA per sample as described in the Affymetrix GeneChip technical analysis manual (Affymetrix UK Ltd, High Wycomb, UK). RNA integrity was checked by an Agilent Bioanalyzer. Microarray experiments were performed in the Affymetrix core lab of Nottingham Arabidopsis Stock Centre, Loughborough, UK. Normalization of raw intensities across all probe sets was performed in R language using Robust Multi-array Average (RMA) algorithms and using Bioconductor software (http://www.bioconductor.org). Three replicates of independently grown material were used.
2017-09-29 | E-MTAB-5748 | biostudies-arrayexpress
Project description:To understand the mechanism of disease progression in psoriasis, we defined Asian small plaque psoriasis (small psoriasis) and Asian intermediate plaque psoriasis (intermediate psoriasis) as psoriasis subtypes with limited disease progression, and compared their cellular and molecular signatures with the classic subtype of Western large plaque psoriasis (large psoriasis; GSE30999). Transcriptome analyses in pre-treatment skin biopsies from patients with Asian small and intermediate plaque psoriasis. 12 Asian small plaque psoriasis skin biopsy tissues (7 lesional and 5 non-lesional skin) and 15 Asian intermediate plaque psoriasis skin biopsy tissues (7 lesional and 8 non-lesional skin). GCRMA (using gcrma package from R/Bioconductor) and adjusted for batch effect. The expression data was combined with Western large psoriasis (GSE30999). Using a normalization based upon quantiles, the expression data was normalized based upon a specified normalization distribution of GSE30999 (see publication for GSE67853). The complete dataset representing: (1) 12 Asian small plaque psoriasis Samples, (2) 15 Asian intermediate plaque psoriasis Samples, and (3) 130 Western large plaque psoriasis Samples from GSE30999 (re-processed), is linked below as a supplementary file.
2016-01-10 | E-GEOD-67853 | biostudies-arrayexpress
Project description:Thalamocortical axons pass through the prethalamus in the first step of their neural circuit formation Although it has been supposed that the prethalamus is an intermediate target for thalamocortical projection formation, much less is known about the molecular mechanisms of this targeting. The samples were grouped into 2 sample types: Olig2-KO and the wild-type. RNA was purified from the E13.5 ventral forebrain from Olig2-KO (Olig2-/-) and the wild-type (Olig2+/+). RNA samples were prepared by pooling RNAs extracted from 3 brains to constitute one replicate and each sample type was prepared in five replicates. cRNA hybridization probes were hybridized to Affymetrix Mouse Whole Genome MOE430 2.0 arrays. The R-CRAN statistical language and Bioconductor software package (Gentleman et al., 2004) were used throughout the expression analyses. Raw image files were processed using Affymetrix GCOS and the Microarray Suite (MAS) 5.0 algorithm. The probe signal levels were quantile-normalized, summarized and then transformed to the log 2 expression using GCRMA (gcrma R-package, Irizarry et al., 2003). Gene filtering was performed using the Wilcoxon signed-rank test to select probe sets that were “consistently expressed” (p <0.04) in at least one group (mas5calls R-package; Bioconductor). All samples showed good quality control according to MAS5.0 guidelines and the AffyQC report (R-package; Bioconductor).
2014-06-04 | E-GEOD-56389 | biostudies-arrayexpress
Project description:We identify a set of common phenotypic modifiers that interact with five independent autism gene orthologs (RIMS1, CHD8, CHD2, WDFY3, ASH1L) causing a common failure of presynaptic homeostatic plasticity (PHP). Heterozygous null mutations in each autism gene are demonstrated to have normal baseline neurotransmission and PHP. However, we find that PHP is sensitized and rendered prone to failure. A subsequent electrophysiology-based genetic screen identifies the first known heterozygous mutations that commonly genetically interact with multiple ASD gene orthologs, causing PHP to fail. Two phenotypic modifiers identified in the screen, PDPK1 and PPP2R5D, are characterized. Finally, transcriptomic, ultrastructural and electrophysiological analyses define one mechanism by which PHP fails; an unexpected, maladaptive up-regulation of CREG, a conserved, neuronally expressed, stress response gene and a novel repressor of PHP. Thus, we define a novel genetic landscape by which diverse, unrelated autism risk genes may converge to commonly affect the robustness of synaptic transmission.
2020-06-26 | GSE153225 | GEO
Project description:To formally address the biological activity of ETS1 in vitro, we measured the transcriptional effect of ETS1 knock down by transducing HPB-ALL leukemia cell lines with a plKO - shETS1 and plko shLUC control. Samples were hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays. Log2 abundance estimates were obtained using gcrma package of Bioconductor, which is a version of the Robust Multi-Array Average (RMA) algorithm. We provide a supplementary file with gene annotation, which performs a two-sample T-test and computes an average fold-change.
2020-07-07 | GSE138803 | GEO
Project description:Gene expression profiling of human promyelocytic cells in response to infection with Anaplasma phagocytophilum. Total RNA derived from 3DPI Anaplasma phagocytophilum-infected HL-60 cells was labeled with A647 and total RNA derived from 3DPI Mock-infected HL-60 cells was labeled with A546. For each, 5 µg of total RNA was labeled using Genisphere Array900, Alexa Fluor dyes and SuperscriptII. Slide scanned with ScanArray Express and images processed with GenePix Pro version 4.0. Normalized log ratios VALUES determined using R-project statistical environment (http://www.r-project.org) and Bioconductor (http://www.bioconductor.org) through the GenePix AutoProcessor (GPAP, http://darwin.biochem.okstate.edu/gpap) website (P. Ayoubi, unpublished results). Keywords: time-course
2005-02-25 | GSE1694 | GEO
Project description:A high percentage of potential oncology drugs fail in clinical trials, partly because preclinical models used to test them are inadequate. Breast cancer is the leading cause of cancer-related death among women worldwide but we lack appropriate in vivo models for the ER+ subtypes, which represent more than 75% of all cases. We address these issues by xenografting tumor cells to their site of origin, the milk ducts. All ER+ cell lines and patient-derived xenografts grow mimicking their clinical counterparts. Disease progresses with invasion and metastasis, which become amenable to study. The action of hormones, important in breast carcinogenesis, can now be studied in a relevant context. Importantly, these open opportunities for development and evaluation of therapies. Eight- to twelve-week-old female SCID Beige mice (Charles River) were injected with 2x10e5 MCF7-DsRed/luc2 cells (n=3) either into the mammary fat pad or 5x10e4 MCF7-DsRed/luc2 cells intraductally (n=3). Xenografted MCF7 were FACS sorting based on DsRed expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included. For each sample, 300 ng of total RNA were amplified using the message amp II enhanced kit (AM1791, Ambion). 12.5 μg of biotin-labelled cRNA were chemically fragmented. Affymetrix GeneChip Human Genome U133A 2.0 Arrays (Affymetrix, Santa Clara, CA, USA) were hybridized with 11μg of fragmented target, at 45°C for 17 hours, washed and stained according to Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007). Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix). All statistical analyses were performed using R and Bioconductor packages (http://www.Bioconductor.org). Hybridization quality was assessed using the Expression Console software (Affymetrix). Normalized expression signals were calculated from Affymetrix CEL files using RMA. Differential hybridized features were identified using Bioconductor package âlimmaâ that implements linear models for microarray data (Smyth, 2004). P values were adjusted for multiple testing with Benjamini and Hochbergâs method to control false discovery rate (FDR) (Benjamini et al., 2001). Probe sets showing â¥2-fold change and a FDR â¤0.05 were considered significant.
2016-03-03 | E-GEOD-68694 | biostudies-arrayexpress