RNAi expression experiments on Illumina BeadChip
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Huck Ng
PROVIDER: E-GEOD-9775 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A core Klf circuitry regulates self-renewal of embryonic stem cells.
Jiang Jianming J Chan Yun-Shen YS Loh Yuin-Han YH Cai Jun J Tong Guo-Qing GQ Lim Ching-Aeng CA Robson Paul P Zhong Sheng S Ng Huck-Hui HH
Nature cell biology 20080210 3
Embryonic stem (ES) cells are unique in their ability to self-renew indefinitely and maintain pluripotency. These properties require transcription factors that specify the gene expression programme of ES cells. It has been possible to reverse the highly differentiated state of somatic cells back to a pluripotent state with a combination of four transcription factors: Klf4 is one of the reprogramming factors required, in conjunction with Oct4, Sox2 and c-Myc. Maintenance of self-renewal and pluri ...[more]
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE9774: Klf2, Klf4, Klf5 and p53 in mouse embryonic stem cells GSE9775: To identify the target genes of Klf2, Klf4 and Klf5 in mouse embryonic stem cells. Keywords: SuperSeries Refer to individual Series
2010-06-25 | E-GEOD-9535 | biostudies-arrayexpress
Project description:Background Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups. Results We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment. Conclusions The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity. Ten MDA-MB-435 samples, biological duplicates of each condition (untreated, integrin Beta4 treatment, hepatocyte growth factor treatment for 1 hr, 6 hrs, or 24 hrs).
2011-08-09 | E-GEOD-26735 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE26732: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Affymetrix) GSE26735: Mulcom: a multiple comparison statistical test for microarray data in Bioconductor (Illumina) Refer to individual Series
2011-08-09 | E-GEOD-26736 | biostudies-arrayexpress
Project description:Although majority of the genes linked to pediatric cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. Here, we identify small Maf transcription factors MafG and MafK as regulators of several non-crystallin human cataract genes in fiber cells and establish their significance to cataract. We applied a bioinformatics tool for cataract gene discovery iSyTE to identify MafG and its co-regulators in the lens, and generated various null-allelic combinations of MafG:MafK mouse mutants for phenotypic and molecular analysis. By age 4-months, MafG-/-:MafK+/- mutants exhibit lens defects that progressively develop into cataract. High-resolution phenotypic characterization of MafG-/-:MafK+/- lens reveals severe defects in fiber cells, while microarrays-based expression profiling identifies 97 differentially regulated genes (DRGs). Integrative analysis of MafG-/-:MafK+/- lens-DRGs with 1) binding-motifs and genomic targets of small Mafs and their regulatory partners, 2) iSyTE lens-expression data, and 3) interactions between DRGs in the String database, unravels a detailed small Maf regulatory network in the lens, several nodes of which are linked to human cataract. This analysis prioritizes 36 highly promising candidates from the original 97 DRGs. Significantly, 8/36 (22%) DRGs are associated with cataracts in human (GSTO1, MGST1, SC4MOL, UCHL1) or mouse (Aldh3a1, Crygf, Hspb1, Pcbd1), suggesting a multifactorial etiology that includes elevation of oxidative stress. These data identify MafG and MafK as new cataract-associated candidates and define their function in regulating largely non-crystallin genes linked to mouse and human cataract. Microarray comparision of lenses from mixed background (129Sv/J, C57BL/6J, and ICR) control (MafG+/-:MafK+/-; no-cataract) and compound (MafG-/-:MafK+/-; cataract) mouse mutants
2015-05-01 | E-GEOD-65500 | biostudies-arrayexpress
Project description:The lung is a branched tubular network with two distinct compartments — the proximal conducting airways and the peripheral gas exchange region — separated by a discrete boundary termed the bronchoalveolar duct junction (BADJ). Here we image the developing mouse lung in three-dimensions and show that two nested developmental waves demarcate the BADJ under the control of a global hormonal signal. A first wave of branching morphogenesis progresses throughout embryonic development, generating branches for both compartments. A second wave of conducting airway differentiation follows the first wave but terminates earlier, specifying the proximal compartment and setting the BADJ. The second wave is terminated by a glucocorticoid signaling: premature activation or loss of glucocorticoid signaling causes a proximal or distal shift, respectively, in BADJ location. The results demonstrate a novel mechanism of boundary formation in complex, three-dimensional organs and provide new insights into glucocorticoid therapies for lung defects in premature birth. RNAs were extracted from E14 lungs cultured in control and dexamethasone media for 24 hours using Trizol reagents and Qiagen RNeasy Micro kit. Two control and two treated samples were analyzed.
2014-05-22 | E-GEOD-56831 | biostudies-arrayexpress
Project description:To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region. Through flow cytometric separation using EpCAM expression to distinguish endoderm from surrounding mesenchyme, pure populations of endoderm progenitors from the esophageal, lung, stomach, pancreatic, and intestinal regions were isolated. Expression of Liv2 was used to isolate a pure population of hepatic endoderm progenitors. Keywords: cell type comparison Three biological replicates each containing dissected organ domains from 10-12 pooled embryos flow cytometrically sorted to isolate endoderm were amplified using Ambion Illumina TotalPrep RNA Amplification kit and arrayed on Illumina MouseRef8 v2 chips
2010-06-24 | E-GEOD-13040 | biostudies-arrayexpress
Project description:Analysis of gene-expression alterations in primitive LT-HSCs as early as 2 days post sex steroid ablation. This study aimed to determine potential intrinsic changes occuring in the LT-HSC population associated with sex steroid ablation (SSA) at a timepoint that preceeded the earliest reported functional hematopoietic enhancements occuring at day 7 post SSA. These results are vital in providing insight into the role of LT-HSCs in initiating SSA-mediated immune regeneration. Total RNA obtained from BM-sorted LT-HSC 2 days after sex steroid ablation compared to sham sex steroid ablation controls.
2015-03-01 | E-GEOD-64841 | biostudies-arrayexpress
Project description:Antigen-specific effector CD8+ T cells deficient in Blimp-1 (Prdm1) do not acquire maximal effector functions, evade terminal differentiation, and more rapidly acquire some hallmark properties of memory CD8+ T cells. In this study, we compared the gene expression profiles of wildtype and Prdm1-/- LCMV-specific effector CD8+ T cells to better understand the molecular mechanisms underlying this striking phenotype. DNA microarray analysis was performed of DbGP33-41 and DbNP396-404 tetramer-positive effector CD8+ T cells FACS-sorted at day 8 post-LCMV infection from four independent samples of either Blimp-1 conditional knockout mice (CKO; Blimp-1flox/flox x GranzymeB-cre+) or wildtype (WT) littermate controls.
2010-08-19 | E-GEOD-17211 | biostudies-arrayexpress
Project description:Pneumonia is a serious problem worldwide. We recently demonstrated that innate defense mechanisms of the lung are highly inducible against pneumococcal pneumonia. To determine the breadth of protection conferred by stimulation of lung mucosal innate immunity, and to identify cells and signaling pathways activated by this treatment, mice were treated with an aerosolized bacterial lysate, then challenged with lethal doses of bacterial and fungal pathogens. Mice were highly protected against a broad array of Gram-positive, Gram-negative, and Class A bioterror bacterial pathogens, and Aspergillus fumigatus. Protection was associated with rapid pathogen killing within the lungs, and this effect was recapitulated in vitro using a respiratory epithelial cell line. Gene expression analysis of lung tissue showed marked activation of NF-kappaB, Type I and II interferon, and antifungal Card9-Bcl10-Malt1 pathways. Cytokines were the most strongly induced genes, but the inflammatory cytokines TNF and IL-6 were not required for protection. Lung-expressed antimicrobial peptides were also highly upregulated. Taken together, stimulated innate resistance (StIR) appears to occur through the activation of multiple host defense signaling pathways in lung epithelial cells, inducing rapid pathogen killing, and conferring broad protection against virulent bacterial and fungal pathogens. Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value for protection of patients with neutropenia or impaired adaptive immunity against opportunistic pneumonia, and for defense of immunocompetent subjects against a bioterror threat or epidemic respiratory infection. Keywords: differential gene expression; time course; innate immunity; pneumonia; immunocompromised host; lung epithelium Gene expression patterns in mouse lung homogenates were analyzed 2h after exposure to aerosolized PBS (Sham treatment), 2h after exposure to aerosolized NTHi lysate or 4h after exposure to aerosolized NTHi lysate. Each group consisted of six mice.
2010-06-24 | E-GEOD-13740 | biostudies-arrayexpress
Project description:Pneumonia is a serious problem worldwide. We recently demonstrated that innate defense mechanisms of the lung are highly inducible against pneumococcal pneumonia. To determine the breadth of protection conferred by stimulation of lung mucosal innate immunity, and to identify cells and signaling pathways activated by this treatment, mice were treated with an aerosolized bacterial lysate, then challenged with lethal doses of bacterial and fungal pathogens. Mice were highly protected against a broad array of Gram-positive, Gram-negative, and Class A bioterror bacterial pathogens, and Aspergillus fumigatus. Protection was associated with rapid pathogen killing within the lungs, and this effect was recapitulated in vitro using a respiratory epithelial cell line. Gene expression analysis of lung tissue showed marked activation of NF-kappa-B, Type I and II interferon, and antifungal Card9-Bcl10-Malt1 pathways. Cytokines were the most strongly induced genes, but the inflammatory cytokines TNF and IL-6 were not required for protection. Lung-expressed antimicrobial peptides were also highly upregulated. Taken together, stimulated innate resistance (StIR) appears to occur through the activation of multiple host defense signaling pathways in lung epithelial cells, inducing rapid pathogen killing, and conferring broad protection against virulent bacterial and fungal pathogens. Augmentation of innate antimicrobial defenses of the lungs might have therapeutic value for protection of patients with neutropenia or impaired adaptive immunity against opportunistic pneumonia, and for defense of immunocompetent subjects against a bioterror threat or epidemic respiratory infection. Keywords: Differential expression, innate immunity, pneumonia, immunocompromised host; lung epithelium, in vitro, MLE-15 cells were treated with sham (PBS), NTHi lysate (100 ug/ml) or EF2505-III (40 ug/ml). 4 unique samples per group. Treated for 2 hours. Hybridized to Illumina Sentrix Mouse-6 v1.1 Beadhips.
2010-06-24 | E-GEOD-13685 | biostudies-arrayexpress