Gene expression microarray analysis of whole intestine from Kaiso-/- mice
Ontology highlight
ABSTRACT: Absence of the epigenetic regulator Kaiso suppresses Wnt driven intestinal tumourigenesis. To identify genes regulated by Kaiso we generated wild type and Kaiso-/- mice for microarray expression analysis to identify genes derepressed in the absence of Kaiso.
Project description:Comparison of the expression profiles of the following genetically altered murine intestinal epithelium: AhCre wildtype, AhCre Apc floxed, AhCre Cited1 null and Ahcre Apcflx/Cited1 null.
Project description:Gene expression were identified with or without CD24 gene silencing in Du145 cells. RNA isolated from 5 independent cultures of Scramble control, 3 cultures of CD24-ShRNA1 and 2 cultures of CD24-ShRNA2 were tested using Affimatrx Human U133 Plus 2.0 microarrays.
Project description:Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose. A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.
Project description:To investigate the role of acrA in antibiotic resistance and pathogenicity this gene was inactivated by insertion of a kanamycin cassette in strain SL1344 and the results on the transcriptome determined.
Project description:To help malaria parasites survive unpredictable host immune responses, it is known that genes for surface proteins express stochastically in Plasmodium falciparum. Here, we demonstrate that gene expression for intracellular metabolic functions may be preordained and insensitive to specific metabolic perturbations. In a tightly-controlled, large microarray study involving over 100 hybridizations to isogenic drug-sensitive and drug-resistant parasites, the lethal antifolate WR99210 failed to over-produce RNA for the biochemically and genetically proven target dihydrofolate reductase-thymidylate synthase (DHFR-TS). Beyond the target, this transcriptional obstinacy carried over to the rest of the parasite genome, including genes for target pathways of folate and pyrimidine metabolism. Even 12 hours after commitment to death, the transcriptome remained faithful to evolutionarily entrained paths. A system-wide transcriptional disregard for metabolic perturbations in malaria parasites may contribute to selective vulnerabilities of the parasite to lethal antimetabolites. While large protective metabolic responses were not detected, DNA microarrays helped capture small, but reproducible drug-dependent perturbations within hours of drug exposure. In addition, in Plasmodium cells that had adapted to long-term drug exposure, DNA microarrays revealed new, large genome-wide transcriptional adjustments in the hard-wired transcriptional program itself. Keywords: Plasmodium falciparum treated with WR99210 RNA from P. falciparum Dd2 and B1G9 (WR99210 resistant cell-line) trophozoites that had been treated with 10 nM WR99210 for varying durations (3, 6, 9, 15, 18, 21 and 24h) was hybridized against a common pool of trophozoite RNA from a cognate clone, a culture containing 0.1% (v/v) DMSO lacking drug was used as untreated control, microarray data were obtained from at least four hybridizations using RNA from two independent parasite cultures
Project description:Lineage commitment during Embryonic Stem Cells (ESCs) differentiation is controlled not only by a gamut of transcription factors but also by epigenetic events, mainly histone deacetylation and promoter DNA methylation. Moreover, the DNA demethylation agent 5′-Aza-2′-deoxycytidine (AzadC) has been widely described in the literature as an effective chemical stimulus used to promote cardiomyogenic differentiation in various stem cell types; however, its toxicity and instability complicate its use. Thus, the purpose of this study was to examine the effects of zebularine, a stable and non-toxic DNA cytosine methylation inhibitor, on ESCs differentiation. Herein are the Affymetrix Expression data obtained from RNA of murine ESCs treated with zebularine. 9 control samples (replicates) and 9 zebularine samples (replicates).
Project description:The aim of this study was to characterize in vivo miRNA expression in normal myeloid development of the neutrophil granulocyte (granulopoiesis) to gain insight into miRNA control of these processes. Cell populations highly enriched in precursors from successive stages of granulopoiesis and mature neutrophils were isolated from bone marrow (BM) and peripheral blood (PB) samples, respectively, from 4 healthy human donors. Total RNA was extracted from each cell population and subjected to miRNA gene expression profiling using miRCURYTM LNA microRNA Arrays Total RNA from cell populations highly enriched in precursors from three succesive stages of neutrophil granulopoiesis and mature neutrophils isolated from bone marrow and peripheral blood, respectively, from four healthy donors (SKP, AJ, AO, JO). The three cell populations from bone marrow where extracted and named B3, B2, and B1, corresponding to immature (myeloblasts [MBs] and promyelocytes [PMs]); intermediate mature (myelocytes [MCs] and metamyelocytes [MMs]); and mature neutrophil cells (band cells [BCs] and segmented neutrophil cells [SCs]), respectively, as described in Bjerregaard MD, Jurlander J, Klausen P, Borregaard N, Cowland JB: The in vivo profile of transcription factors during neutrophil differentiation in human bone marrow. Blood 2003, 101: 4322-4332. In total, 16 samples were compared (4 cell maturation stages from 4 donors)
Project description:Sky1 is a Saccharomyces cerevisiae rich serine-arginine (SR) protein-specific kinase and its enzymatic activity is essential in the cytotoxicity caused by cisplatin, although the molecular mechanisms supporting this function are not understood. We present a transcriptome analysis discriminating between RNA changes induced by cisplatin which are dependent or independent of the Sky1 function. The S. cerevisiae strain W303 (MATa ade2-1 can1-100 leu2-3,112 trp1-100 ura3- 52) and its derivative W303-M-NM-^Tsky1 previously described (RodrM-CM--guez- Lombardero et al., 2012) have been used in these analyses. Biological replicates of cultures and treatments were run in triplicate. The yeast cells were pre-cultured over night in 10mL of complete synthetic medium (SD) prepared as previously described (Zitomer and Hall, 1976). The following day the cells were inoculated at initial OD600 of 0.4 in 70 mL SD and grown in 250 mL Erlenmeyer flasks at 30 M-BM-:C and with agitation at 250 rpm. When cells reached OD600 of 0.6, the cultures from each strain were divided in two aliquots of 25 mL (control and cisplatin treatment). A stock solution of cisplatin 6 mM in dimethyl sulfoxide (DMSO) was prepared and the drug was added to the treated cultures at a final concentration of 600 microM. An equivalent volume of DMSO was added to the control cultures. The treatment was done at 30M-BM-:C and with agitation at 250 rpm during four hours in darkness. RNA was extracted from a number of cells corresponding to OD600 of 3 with the AurumTM Total RNA Mini Kit (Bio-Rad) and following the manufacturerM-bM-^@M-^Ys instructions. The RIN parameter (RNA Integrity Number) evaluated with the 2100 was near to the value 9 in all the samples. Three different RMA analyses were performed: Analysis 1: GSM1008483-GSM1008488 Analysis 2: GSM1008489-GSM1008494 Analysis 3: GSM1008495-GSM1008500