Comparative analysis of gene expression profiles between Nodal-overexpressing embryos with control embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Ciona intestinalis
SUBMITTER: Ryo Koyanagi
PROVIDER: E-GEOD-14567 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In the two F8 advanced crosses of broiler by Leghorn and broiler by Fayoumi, birds at day 1 were challenged with Salmonella enteritidis (SE). Spleen were collected at day 7 and 8. SE bacterial load in spleen were measured. Based on the bacterial load, birds were divided into high and low SE load groups. At each line cross and each day time point, three pair comparisons among high SE load, low SE load, and non-SE were used for the loop design, and two biological replicates were used.
2010-07-01 | E-GEOD-4273 | biostudies-arrayexpress
Project description:Neural stem cells (NSCs) can be isolated from different regions of the central nervous system. There has been controversy whether regional differences amongst stem and progenitor cells are cell intrinsic and whether these differences are maintained during expansion in culture. The identification of inherent regional differences has important implications for the use of these cells in neural repair. Here, we compared neural stem cells derived from the spinal cord and embryonic cortex. We found that while cultured cortical and spinal cord derived neural stem cells respond similarly to mitogens and are equally neuronogenic, they retain and maintain through multiple passages gene expression patterns indicative of the region from which they were isolated. Further microarray analysis identified 229 genes that were differentially expressed between cortical and spinal cord derived neurospheres. Experiment Overall Design: Cortex and and spinal cords were isolated from embryonic day 14 cd1 mice and cultured ad neurospheres for 2 passages in EGF and bFGF. 3 independent sets of cultures serve as biological replicates with a dye flip control for each hybridization, for a total of 6 arrays.
2009-02-20 | E-GEOD-9433 | biostudies-arrayexpress
Project description:To identify regions that display DNA copy number alterations in malignant pleural mesothelioma (MPM), we carried out array comparative genomic hybridization (CGH) analysis with 14 MPM cell lines. Regions of genomic aberrations observed in >20% of individuals were 9p21.3, 13q12.11, 16p13, and 22q12.2 of losses. The most frequent alteration was 9p21.3, which include the p16INK4/p14ARF. The loss of 22q12.2 regions include the NF2 was observed in 3 out of 14 cell lines. In 3 cell lines, loss of 13q12.11 region which contains Large Tumor Suppressor, homolog 2 (LATS2) was detected. Human malignant pleural mesothelioma cell lines were profiled on Agilent 244K aCGH arrays according to manufacturer’s instructions. Pooled normal human genomic DNA was used as the reference.
2010-06-15 | E-GEOD-22237 | biostudies-arrayexpress
Project description:Tumor angiogenesis requires intricate regulation of gene expression in endothelial cells (EC). We recently showed that DNA methyltransferase (DNMT)- and histone deacetylase (HDAC) inhibitors directly repress EC growth and tumor angiogenesis, suggesting that epigenetic modifications mediated by DNMTs and HDACs are involved in regulation of EC gene expression during tumor angiogenesis. To understand the mechanisms behind the epigenetic regulation of tumor angiogenesis, we used microarray analysis to perform a comprehensive screen to identify genes downregulated in tumor-conditioned versus quiescent EC, and re-expressed by 5-aza-2â-deoxycytidine and trichostatin A. Among the 81 genes identified, 77% harboured a promoter CpG island. Validation of mRNA levels of a subset of genes confirmed significant downregulation in tumor-conditioned EC and reactivation by treatment with a combination of 5-aza-2â-deoxycytidine and trichostatin A, as well as by both compounds separately. Silencing of these genes in tumor-conditioned EC correlated with promoter histone H3 deacetylation and loss of H3 lysine 4 methylation, however did not involve DNA methylation of promoter CpG islands. For six genes, downregulation in microdissected human tumor endothelium was confirmed. Functional validation by RNA interference revealed that clusterin, fibrillin 1 and quiescin Q6 are negative regulators of EC growth and angiogenesis. In summary, our data identify novel angiogenesis suppressing genes which become silenced in tumor-conditioned EC in association with promoter histone modifications and reactivated by DNMT- and HDAC inhibitors through reversal of these epigenetic modifications, providing a mechanism for epigenetic regulation of tumor angiogenesis. Experiment Overall Design: A commercial pool (a mixture of 32 donors) of HUVEC (Tebu-bio, Heerhugowaard, The Netherlands) was used for DNA microarray experiments. Total RNA was isolated using the RNeasy RNA isolation kit (Qiagen) according to the supplier's protocol. Possible genomic DNA contaminations were removed by on column DNase treatment with the RNase-free DNase set (Qiagen). The purified RNA was quantified using a Nanodrop spectrophotometer, and RNA quality was evaluated using the Agilent 2100 Bioanalyzer. cDNA synthesis was performed using the Agilent Fluorescent Direct Labelkit with direct incorporation of either cyanine 5 (Cy5) or Cy3 âdCTP nucleotides (Perkin Elmer) according to the manufacturerâs instructions. Labeled cDNA was purified using QIAquick PCR purification columns (Qiagen), followed by concentration by vacuum centrifugation. The Agilent human 1A cDNA microarray (Agilent Technologies, Amstelveen, The Netherlands) contained ~15000 cDNA probes. Labeled cDNA was resuspended in hybridisation buffer and hybridised to Agilent human 1A cDNA microarray for 17 h at 65°C, according to the Agilent protocols. All hybridisations were replicated with cy dyes switched. Two fluorescent microarray comparisons were performed: (1) A comparison of tumor-conditioned HUVEC and quiescent HUVEC and (2) a comparison of tumor-conditioned HUVEC treated with or without a combination of DAC and TSA. Experiment Overall Design: Microarray data processing and statistical analysis Experiment Overall Design: The image file was processed using Agilent's Feature Extraction software (version A.6.1.1, Agilent Technologies). This Feature Extraction program was used to identify pixels corresponding to fluorescent signal (as opposed to background) and to remove pixels with intensities that met the default criteria for outliers. The different normalisation routines applied (Local Background, Minimum signal (feature or background) & Average of all background areas) resulted in comparable results. For each identified area of signal and each of the two dyes, the basic measure of RNA abundance was taken to be the mean intensity over pixels in the identified signal area. The log ratio of the red to green intensities for each signal area was used for statistical analyses, with all subsequent analyses done using the R statistical software package (version 1.2). We selected fold change 1.5 as a threshold, since the 4 hybridisations increase the likelihood of statistical reliability.
2008-06-15 | E-GEOD-7132 | biostudies-arrayexpress
Project description:mutants in the stalk biogenesis and sigma-54 pathways deletion mutants of each component were compared to wild type, with all strains grown to mid-log phase as mixed populations
2006-04-05 | E-GEOD-3328 | biostudies-arrayexpress
Project description:Kallikrein-related peptidase 3 (KLK3, also known as prostate-specific antigen, PSA) is a chymotrypsin-like kallikrein that has been shown to have anti-angiogenic properties. KLK3 expression in prostate cancer is associated with low microvessel density. We have previously shown in a human umbilical vein endothelial cell (HUVEC) model that the anti-angiogenic effect of KLK3 is related to its enzymatic activity. However, the mechanism of this effect remains to be clarified. To this end we have used a DNA microarray to study the KLK3-induced changes in gene expression associated with reduction of HUVEC tube formation. Among the 41000 genes studied, 311 were differentially expressed in control and KLK3-treated cells. These changes were enriched in several pathways, including the pathways associated with proteasome, ubiquitin-mediated proteolysis, focal adhesion and regulation of actin cytoskeleton. Furthermore, the changes were opposite to those described previously to occur during tubulogenesis. In conclusion, our results show that KLK3 induces gene expression changes in HUVECs. While these changes might be relevant for the mechanism by which KLK3 exerts its anti-angiogenic activity, it cannot be judged by the present results whether the changes are secondary to morphogenic differentiation of the cells or the primary mechanism mediating the effect of KLK3. Keywords: KLK3 treatment, tube formation Human umbilical vein endothelial cells (HUVECs) were isolated from umbilical cord veins and grown in Endothelial Cell Basal Medium supplemented with an Endothelial Cell Growth Medium Supplement Pack (PromoCell). The cells were cultured on Matrigel basement membrane prepara-tion together with 500 nM enzymatically active KLK3 (PSA). Phosphate buffered saline (PBS) was used for control. HUVECs were grown on Matrigel for 18 h. RNA was isolated from KLK3-treated and control HUVECs from three different individuals. Cell Recovery Solution (BD Biosciences) was used to detach cells from the Matrigel. Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to manufacturerâ??s instructions. RNA con-centration and quality of the samples was determined with an Agilent 2100 bioanalyser (Agilent Technologies) by measuring the RNA integrity number (RIN). All samples contained high quality RNA (RIN 9.5-10). DNA microarray analysis was performed with the Agilent Whole Human Genome Oligo Microar-ray 4x44K (G4112F) (Agilent Technologies Inc.) following the manufacturerâ??s protocol. Total RNA (1 ï?g) was labeled using the RNA input fluorescent linear amplification kit according to the manufacturer's recommendations (Agilent Technologies Inc.). RNA was hybridized on Agilent's Human 4x44K Oligo Microarrays containing 44000 features (41000 unique genes and transcripts). Pre-processing of the data was performed by Feature Extraction software (v 7.5.1).
2010-06-25 | E-GEOD-9869 | biostudies-arrayexpress
Project description:We have compared the changes in cell cycle and cell death parameters induced by 2 different concentrations of 5-FU (IC50 and IC80) in the breast adenocarcinoma cell line MCF7. G1/S cell cycle arrest was associated with both concentrations, whereas cell death was mainly induced after IC80 5-FU. These changes were correlated with gene expression assessed by cDNA microarray analysis. Main findings included an overexpression of p53 target genes involved in cell cycle and apoptosis (CDKN1A/p21, TP53INP, TNFRSF6/FAS and BBC3/PUMA), and significant repression of Myc. High dose 5-FU also induced a higher regulation of the mitochondrial death genes APAF1, BAK1 and BCL2, and induction of genes of the ID family. Time and dose-dependent changes in gene expression, induced by 5-Fluorouracil, in breast carcinoma cell lines MCF7, and MDA-MB-435.
2010-07-01 | E-GEOD-2584 | biostudies-arrayexpress
Project description:Despite the recognized protective effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in cardiovascular diseases, and the demonstration of the control of gene expression by polyunsaturated fatty acids (PUFAs), the effects of these n-3 fatty acids on the whole genoma has never been investigated in cardiac cells. Using rat arrays, the effects of Eicosapentaenoic acid (EPA) and Docosahexaenoic acid (DHA) supplementation on the global gene expression profile were evaluated in cultured neonatal rat cardiomyocytes. Experiment Overall Design: Primary cardiomyocyte cultures were obtained from the ventricles of newborn Wistar rats and grown in HAM F10 plus 10% fetal calf serum and 10% horse serum medium (controls), or in the same medium supplemented with 60 ïM Eicosapentaenoic acid (EPA) or docosahexaenoic acid (DHA). Media were changed every 48 hrs; cells were grown until complete confluence, then they were scraped off in ice cold PBS, and RNA isolation, labeling of complementary RNA (cRNA), hybridization to Agilent 22K-gene arrays (Rat oligo array G4130A) and assessment of expression ratios were performed. About one million cells treated with RNAlater were homogenized and total RNA was extracted by column technology (Rneasy Protect mini kit) and analyzed on both a spectrophotometer and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). Only samples with 28S/18S ratio of >2.0 and no evidence of ribosomal peak degradation were included. The cRNA was generated by in vitro transcription with the use of T7 RNA polymerase (Low RNA input fluorescent linear amplification kit) and labeled with Cy3-CTP or Cy5-CTP. Direct comparisons were performed between n-3 PUFAs supplemented cells versus unsupplemented ones (controls); each analysis was replicated swapping the labeling with the two cyanine dyes.
2008-05-07 | E-GEOD-4327 | biostudies-arrayexpress
Project description:chpT depletion ML808 versus wild type CB15N three independent colonies were grown to mid-log phase in PYE + xylose and RNA harvested for analysis on microarrays
2010-07-01 | E-GEOD-4617 | biostudies-arrayexpress
Project description:Several genes involved in nitrogen metabolism are known to contribute to the virulence of pathogenic bacteria. Here, we studied the function of the nitrogen regulatory protein GlnR in the Gram-positive human pathogen Streptococcus pneumoniae. We demonstrate that GlnR mediates transcriptional repression of genes involved in glutamine synthesis and uptake (glnA, glnPQ), glutamate synthesis (gdhA), and the gene encoding the pentose phosphate pathway enzyme Zwf, which forms an operon with glnPQ. Moreover, the expression of gdhA is also repressed by the pleiotropic regulator CodY. The GlnR-dependent regulation occurs through a conserved operator sequence and is responsive to the concentration of glutamate, glutamine and ammonium in the growth medium. By means of in vitro binding studies and transcriptional analyses we show that the regulatory function of GlnR is dependent on GlnA. Mutants of glnA and glnP displayed significantly reduced adhesion to Detroit 562 human pharyngeal epithelial cells, suggesting a role for these genes in the colonization of the host by S. pneumoniae. Thus, our results provide a thorough insight into the regulation of glutamine and glutamate metabolism of S. pneumoniae as mediated by both GlnR and GlnA. Each amplicon was spotted twice (technical replicates) on the DNA microarray. These replicates are indicated in the platforms and DNA microarray data by the addition of _rep1, _rep2, etc. The RNA for wild-type and mutant strains was isolated in 3 independent biological replicates which were hybridized in (partly dye-swap) to the 3 slides for glnA and 3 slides for glnR.
2010-07-01 | E-GEOD-5088 | biostudies-arrayexpress