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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from cid14 delta and air1 delta strains

ABSTRACT: Expression profiling of cid14 delta and air1 delta cells shows that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1. Gene expression in the mutants was compared to the parent wild-type strain. 2 biological replicates were performed for each strain.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Katrina Woolcock

PROVIDER: E-GEOD-20905 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from cid14 delta and air1 delta strains

Project description:Expression profiling of cid14 delta and air1 delta cells shows that efficient silencing of a few heterochromatic genes depends on Cid14 and/or Air1.

2010-03-17 | GSE20905 | GEO

PRC1 coordinates timing of sexual differentiation of female primordial germ cells

Project description:In mammals, sex differentiation of primordial germ cells (PGCs) is determined by extrinsic cues from the environment1. In female PGCs, expression of Stimulated by retinoic acid 8 (Stra8) and meiosis are induced in response to retinoic acid (RA) provided by the mesonephroi2-4. Given the widespread role of RA signaling during development8,9, the molecular mechanism specifying the competence of PGCs to timely express Stra8 and enter meiosis are unknown2,10. Here we identify gene dosage dependent roles in PGC development for Ring1 and Rnf2, two central components of the Polycomb Repressive Complex 1 (PRC1)11,13. Both paralogs are essential for PGC development between day 10.5 and 11.5 of gestation. Rnf2 is subsequently required in female PGCs for maintaining high levels of Oct4 and Nanog expression6, and for preventing premature induction of meiotic gene expression and entry into meiotic prophase. Chemical inhibition of RA signaling partially suppresses precocious Oct4 down-regulation and Stra8 activation in Rnf2-deficient female PGCs. Chromatin immunoprecipitation analyses show that Stra8 is a direct target of PRC1 and PRC2 in PGCs. These data demonstrate the importance of PRC1 gene dosage in PGC development and in coordinating the timing of sex differentiation of female PGCs by antagonizing extrinsic RA signaling. Gene expression of mouse primordial germ cells was analysed using Affymetrix microarray. Primodial germ cells were purified from embryos carrying Oct4(deltaPE)-GFP transgene by FACS.

2013-03-14 | E-GEOD-42782 | biostudies-arrayexpress

Early parity-induced gene expression in total mammary epithelial cells in mice

Project description:This study examined the effect of early pregnancy on the gene expression profile of total isolated mammary epithelial cells in mice. Total mammary epithelial cells were isolated from parous and age-matched virgin control mice. Four independent replicates were assessed per treatment group, resulting in a total of 8 samples.

2013-03-17 | E-GEOD-40876 | biostudies-arrayexpress

Early parity-induced gene expression in mouse mammary cell subtypes

Project description:This study examined the effect of early pregnancy on the gene expression profiles of stromal and various epithelial mammary cell subpopulations in mice. Mammary cell subpopulations were isolated from parous and age-matched virgin control mice. Three independent replicates were assessed per cell subpopulation and treatment group, resulting in a total of 35 samples.

2013-03-17 | E-GEOD-40875 | biostudies-arrayexpress

Early parity-induced gene expression in total mammary epithelial cells and mammary cell subtypes in mice

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-03-17 | E-GEOD-40877 | biostudies-arrayexpress

Transcriptional profiling of CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains in the absence or presence of alpha pheromone in Candida albicans

Project description:Twenty-one pheromone-induced genes were selected from the literature (Zhao, Daniels et al. 2005 was the major source) as the reference set for assessing the pheromone response of CAI4 (Wild-type), cpp1Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains.Our aim was to check whether or not these 21 pheromone-induced genes are up-regulated in response to pheromone in each mutant strain.

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Expression analysis of Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp and B. fragilis NCTC 9343 delta-lfg

Project description:Investigation of whole genome gene expression level changes in a Bacteroides fragilis NCTC 9343 delta-gmd-fcl delta-fkp mutant strain and a Bacteroides fragilis NCTC 9343 delta-lfg mutant strain, each as compared to the wild-type strain. The mutations engineered into these strains interfere with B. fragilis protein glycosylation.

2010-08-06 | GSE12440 | GEO

Expression data from U373 cells expressing EGFP, MAML1-dn and DTX1-myc

Project description:Glioblastoma multiforme (GBM) is the most malignant and most common tumor of the central nervous system characterized by rapid growth and extensive tissue infiltration. GBM results in more years of life lost than any other cancer type. Notch signaling has been implicated in GBM pathogenesis through several modes of action. Inhibition of Notch leads to a reduction of cancer-initiating cells in gliomas and reduces proliferation and migration. Deltex1 (DTX1) is part of an alternative Notch signaling pathway distinct from the canonical MAML1/RBPJŒ∫-mediated cascade. In this study, we show that DTX1 activates both the RTK/PI3K/PKB as well as the MAPK/ERK pathway. Moreover, we found the anti-apoptotic factor Mcl-1 to be induced by DTX1. In accordance with this, the clonogenic potential and proliferation rates of glioma cell lines correlated with DTX1 levels. DTX1 knock down mitigated the tumorigenic potential in vivo, and overexpression of DTX1 increased cell migration and invasion of tumor cells accompanied by an elevation of the pro-migratory factors PKBŒ≤ and Snail1. Microarray gene expression analysis identified a DTX1-specific transcriptional program - including microRNA-21 - which is distinct from the canonical Notch signaling. We propose the alternative Notch pathway via DTX1 as oncogenic factor in malignant glioma and found low DTX1 expression levels to correlate with prolonged survival of GBM and early breast cancer patients in open source databases. We generated human glioma U373 cell lines stably expressing Enhanced Green Fluorescent Protein (EGFP), human Deltex1-Myc Tag (DTX1-myc), or Master Mind Like 1 - dominant negative (MAML1-dn) to compare differences in overall gene expression. We included 3x EGFP control samples, 3x DTX1-myc, and 3 MAML1-dn samples.

2012-05-31 | E-GEOD-22772 | biostudies-arrayexpress

Transcriptome analysis of hpl-2(tm1489) vs wild-type worms at mixed embryonic and third larval stages

Project description:Epigenetic factors guide cell fate decisions and can stabilize development by buffering environmental variation. HP1 proteins have a well-characterized role in heterochromatin packaging and gene regulation, while their function in organismal development is less well understood. Here we used genome-wide expression profiling to assess novel functions of the C. elegans HP1 homologue HPL-2 at specific developmental stages RNA was extracted from either mixed-stage embryos or from third larval stage worms for both wild-type N2 (Bristol) and hpl-2(tm1489) strains.

2011-11-30 | E-GEOD-33700 | biostudies-arrayexpress

An Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer

Project description:Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. In contrast, disruption of zinc coordination renders Dcr1 mainly cytoplasmic and leads to remarkable changes in gene expression and loss of heterochromatin assembly. In summary, our results reveal novel insights into the mechanism of nuclear retention of Dcr1 and raise the possibility that this new class of dsRBDs might generally function in nucleo-cytoplasmic trafficking and not substrate binding. The C-terminal domain of Dcr1 constitutes a novel regulatory module that might represent a potential target for therapeutic intervention with fungal diseases. 12 chips representing 4 different strains. Every condition is represented by three biological replicates

2011-09-22 | E-GEOD-30586 | biostudies-arrayexpress

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