Small hydrophobic protein of human metapneumovirus does not affect virus replication and host gene expression in vitro
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Arno Andeweg
PROVIDER: E-MTAB-1152 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The transition between morula and blastocyst stage during preimplantation development represents the first differentiation event of embryogenesis. Morula cells undergo the first cellular specialization and produce two well-defined populations of cells, the trophoblast and the inner cell mass (ICM). Embryonic stem cells (ESCs) with unlimited self-renewal capacity are believed to represent the in vitro counterpart of the ICM. Both mouse and rat ESCs can be derived from the ICM cells, but their in vitro stability differs. In this study we performed a microarray analysis in which we compared the transcriptome of mouse and rat morula, blastocyst, and ICM. This cross-species comparison represents a good model for understanding the differences in derivation and cultivation of ESCs observed in the two species. In order to identify alternative regulation of important molecular mechanisms the investigation of differential gene expression between the two species was extended at the level of signaling pathways, gene families, and single selected genes of interest. Some of the genes differentially expressed between the two species are already known to be important factors in the maintenance of pluripotency in ESCs, like for example Sox2 or Stat3, or play a role in reprogramming somatic cells to pluripotency like c-Myc, Klf4 and p53 and therefore represent interesting candidates to further analyze in vitro in the rat ESCs. This is the first study investigating the gene expression changes during the transition from morula to blastocyst in the rat preimplantation development. Our data show that in the pluripotent pool of cells of the rat and mouse preimplantation embryo substantial differential regulation of genes is present, which might explain the difficulties observed for the derivation and culture of rat ESCs using mouse conditions Casanova EA, Okoniewski MJ, Cinelli P. Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos.PLoS One. 2012;7(10):e47107. doi: 10.1371/journal.pone.0047107. Epub 2012 Oct 15. We collected morula and blastocysts stage embryos from mouse and rat and, by immunosurgery, we isolated the ICM cells from the blastocysts. All the embryos and ICMs were pooled into two groups for every developmental stage. Pooling of embryos for RNA extraction in this study was chosen mainly because of the low amounts of RNA that can be isolated from preimplantation embryos, and in addition because of the heterogeneity of the cell populations present in the embryos. For the analysis we pooled a large number (n >100) of the independent isolated embryos to achieve a sufficient accuracy of biological pooling . Due to the difficulties to isolate a larger number of embryos from mice and rats, we performed the microarray study by using two replicate samples per developmental stage.
2012-11-07 | E-GEOD-42081 | biostudies-arrayexpress
Project description:The aim of this study was to determine the role that miRNAs have on influencing murine microgial phenotypes under M1(LPS) and M2a (IL-4) stimulating conditions. This Series includes expression data obtained from mRNA gene expression microarrays; miRNA expression profiles obtained from the same RNA samples were deposited as a separate Series. 9 total samples were analyzed, n=3 for the three stimulating conditions (resting state, LPS and IL-4) for murine primary microglia. This allowed us to perform the following pairwise comparisons: PBS vs. LPS, and PBS vs. IL-4. This was performed for both mRNA and miRNA gene expression profiles.
2014-03-13 | E-GEOD-49329 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-03-13 | E-GEOD-49331 | biostudies-arrayexpress
Project description:While the response to G-CSF is a significant predictor of AML outcome, the nature of cells responding differentially to this and other cytokines remains unclear. Based on gene expression signatures observed in G-CSF Responsive Cells (RC) and non-G-CSF Responsive Cells (NRC) a cohort of AML samples were segregated into two types. In Type1 both cell subsets displayed an undifferentiated phenotype. In the Type2 AML the RC showed a very similar undifferentiated progenitor-like phenotype as in Type1 RC, whereas the NRC exhibited a more differentiated hematopoietic phenotype. The frequency of RC per sample was a determinant of whether a patient belonged to Type1 or Type2. Type2 RC had higher expression of CD321, higher colony formation capacity and greater responsiveness to cytokines secreted by NRC. Further analysis of clinical mRNA databases revealed that CD321 was a prognostic indicator for AML and a potential marker of clonogenic activity associated with this AML cancer lineage. Cryopreserved PBMC from 11 AML patinets were stimulated with G-CSF. Following stimulation cells were fixed, permeabilized and stained for selected surface markers (CD3, CD33, CD45) and and phospho-Stat3/5. After staining subsets positive and negative for phospo-Stat3/5 were sorted out for further microarray analysis. T-cells were sorted from each sample to control for the RNA quality by comparisons to RNA prepared from live T-cells sorted form healthy donors.
2013-01-09 | E-GEOD-42140 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-05-01 | E-GEOD-57878 | biostudies-arrayexpress
Project description:The glucocorticoid receptor overexpression in early life is sufficient to alter gene expression patterns for the rest of the animal's life. Hippocampal dentate gyrus (DG) are more responsive than the nucleus accumbens (NAcc) following the glucocorticoid receptor overexpression in the forebrain. Laser capture microdissection was performed. Microdissected areas from the dentate gyrus or nucleus accumbens were collected from serial sections for each animal.
2012-03-15 | E-GEOD-30187 | biostudies-arrayexpress
Project description:Human liver progenitor cells (LPCs) show therapeutic potential, however, their in vitro culture results in inadequate function and phenotypic instability reflecting incomplete understanding of in vivo processes. Foetal LPCs capable of differentiation to a hepatocyte phenotype were isolated and mRNA expression profiling carried out using Affymetrix HGU133plus2 microarrays. This was compared to profiles from mature human hepatocytes and human embryonic stem cells undergoing hepatocytic differentiation. Foetal LPCs exhibit a distinct molecular profile consistent with a stem cell signature, cell division, and some liver-specific functions. 9 independent samples of second trimester liver progenitor cells were profiled along with 3 independent mature hepatocyte samples and 3 each of embryonic stem cells at day 9 and day 17 of differentiation to hepatocyte like cells.
2015-05-01 | E-GEOD-57812 | biostudies-arrayexpress
Project description:The oncogenic transcription factor TAL1/SCL is aberrantly overexpressed in over 40% of cases of T-cell acute lymphoblastic leukemia (T-ALL), emphasizing the importance of the TAL1-regulated transcriptional program in the molecular pathogenesis of T-ALL. Here we identify the core transcriptional regulatory circuit controlled by TAL1 and its regulatory partners HEB, E2A, GATA3, ETS1 and RUNX1 in T-ALL cells. We find that TAL1 forms an interconnected auto-regulatory loop with its partners, which contributes to the sustained upregulation of its direct target genes. Importantly, we also find the MYB oncogenic transcription factor is directly activated by the TAL1 complex and positively regulates many of the same target genes, thus forming a feed-forward positive regulatory loop that further promotes the TAL1-regulated oncogenic program. Two experiments were performed: 1. Duplicate hairpins for each transcription factor (TAL1, TCF12/HEB, TCF3/E2A, GATA3, MYB) and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat) 2. Duplicate hairpins for RUNX1 and control hairpins (GFP and Luciferase) were used to idenfity the expression change in the T-ALL cell line (Jurkat)
2012-08-16 | E-GEOD-29179 | biostudies-arrayexpress
Project description:Genomic studies in chronic myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS) and MPN/MDS, have identified common mutations in genes encoding signaling, epigenetic, transcription and splicing factors. Analysis of 18 of these genes in a cohort of 224 chronic myelomonocytic leukemias (CMML), which is the most frequent MPN/MDS, identified at least one mutated gene in 95% of the patients, with some of the mutations affecting the disease phenotype. The number of mutated genes negatively affected progression-free and overall survival in multivariate analysis. Analysis of sorted progenitors indicated an early amplification of the CMML clone at the CD34+/CD38- stage of hematopoiesis, together with a premature granulomonocytic differentiation skewing. We interrogated the clone architecture by mutation-specific discrimination analysis of single-cell-derived colonies. The genetic classification of individual colonies allowed a designation of sub-clones and the assembly of putative evolutionary trees, indicating a linear acquisition of the studied mutations. Analysis of matched pre- and post-treatment samples demonstrated clonal persistence with limited and selective elimination of sub-clones. The disease was characterized by an amplification of multipotent and common myeloid progenitors in the CD34+ compartment, both fractions showing increased granulomonocytic differentiation at the expense of erythroid progenitors, contrasting with normal granulomonocytic progenitors. Altogether, early amplification of the leukemic clone and increased granulomonocytic differentiation of early progenitors may account for the specificity of CMML among myeloid neoplasms. This experiment correspond to the analysis of gene expression profiles in total CD34+ cells from the peripheral blood of 15 patients (Chronic Myelomonocytic Leukemia) and 4 healthy controls.
2013-01-17 | E-MTAB-1044 | biostudies-arrayexpress
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