Transcription profiling of mouse Sox6 mutant skeletal muscle
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Nobuko Hagiwara
PROVIDER: E-MEXP-400 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostate cancer (CRPC). However, the determinants of AR overexpression in CRPC are poorly defined. Here we show that retinoic acid receptorârelated orphan receptor γ (ROR-γ) is overexpressed and amplified in metastatic CRPC tumors, and that ROR-γ drives AR expression in the tumors. ROR-γ recruits nuclear receptor coactivator 1 and 3 (NCOA1 and NCOA3, also known as SRC-1 and SRC-3) to an ARâROR response element (RORE) to stimulate AR gene transcription. ROR-γ antagonists suppress the expression of both AR and its variant AR-V7 in prostate cancer (PCa) cell lines and tumors. ROR-γ antagonists also markedly diminish genome-wide AR binding, H3K27ac abundance and expression of the AR target gene network. Finally, ROR-γ antagonists suppressed tumor growth in multiple AR-expressing, but not AR-negative, xenograft PCa models, and they effectively sensitized CRPC tumors to enzalutamide, without overt toxicity in mice. Taken together, these results establish ROR-γ as a key player in CRPC by acting upstream of AR and as a potential therapeutic target for advanced PCa. A total of 6 samples were analyzed in this study. The study included one cell line C4-2B. C4-2B cells were cultured in medium containing vehicle control and/or SR2211 and/or XY011 and/or Enzalutamide (ENZ). The untreated C4-2B cells served as controls for the study.
2016-03-08 | E-GEOD-72483 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-11-24 | E-GEOD-70934 | biostudies-arrayexpress
Project description:We report the effects of 1,25(OH)2D3 treatment on the mRNA expression in human muscle cells Primary cultures of human muscle cells were treated with 1,25(OH)2D3 or vehicle for 48 hours.
2015-11-24 | E-GEOD-68323 | biostudies-arrayexpress
Project description:In eukaryotic cells, inefficient splicing is surprisingly common and leads to degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here we uncover a mechanism by which intronic transcripts are targeted for nuclear degradation in fission yeast. Surprisingly, sequence elements within âsuicidalâ introns co-transcriptionally recruit the exosome adaptor Mmi1 not only to degrade unspliced precursor, but also to downregulate levels of the resulting mRNA. Under conditions permissive for fast splicing, Mmi1 is no longer recruited and negative expression regulation is relieved. This mechanism negatively regulates levels of the RNA-helicase DDX5/Dbp2 to ensure cell survival in response to stress. We propose that suicidal introns are maintained because they facilitate regulation of gene expression. We identify multiple novel Mmi1 targets including mRNAs, non-coding RNAs, and sn/snoRNAs. We suggest a general role in RNA regulation for Mmi1 beyond degradation of meiotic transcripts. Two biological replicates of CRAC experiments (Control and Mmi1-HTP). Six RNAseq datasets in total: three biological replicates of wt and delta Mmi1 strain.
2015-11-19 | E-GEOD-73144 | biostudies-arrayexpress
Project description:Transcriptional profiling of human T cells analyzing the impact of race on the responsiveness to IFNa in healthy blood donors. Control and IFNa-treated samples derived from healthy Caucasian American vs. African American blood donors are compared. Two-condition experiment, Control vs. IFNa-treated. Paired design; untreated and treated samples for each donor.
2010-05-16 | E-GEOD-17952 | biostudies-arrayexpress
Project description:Epigenetic and metabolic reprogrammings are implicated in cancer progression with unclear mechanisms. We report here that the histone methyltransferase NSD2 drives cancer cell and tumor resistance to therapeutics such as tamoxifen, doxorubicin, and radiation by reprogramming of glucose metabolism. NSD2 coordinately up-regulates expression of TIGAR, HK2 and G6PD and stimulates pentose phosphate pathway (PPP) production of NADPH for ROS reduction. We discover that elevated expression of TIGAR, previously characterized as a fructose-2,6-bisphosphatase, is localized in the nuclei of resistant tumor cells where it stimulates NSD2 expression and global H3K36me2 mark. Mechanistically, TIGAR interacts with the antioxidant regulator Nrf2 and facilitates chromatin assembly of Nrf2-H3K4me3 methylase MLL1 and elongating Pol-II, independent of its metabolic enzymatic activity. In human tumors, high levels of NSD2 correlate strongly with early recurrence and poor survival and are associated with nuclear-localized TIGAR. This study defines a nuclear TIGAR-mediated, epigenetic autoregulatory loop functioning in redox rebalance for resistance to tumor therapeutics. A total of 4 samples were analyzed in this study. The study included two cell lines, MCF7 and the tamoxifen-resistant subline TMR. Both were were cultured in medium containing vehicle control and/or 4-hydroxytamoxifen (Tam). The untreated MCF7 and TMR cell lines served as controls for the study.
2016-10-22 | E-GEOD-62613 | biostudies-arrayexpress
Project description:Therapies targeting the androgen receptor are critical for treatment of hormone refractory prostate cancer. We have previously demonstrated that Ebp1, a protein isolated by its ability to bind ErbB3, is a downstream effector of heregulin activated pathways and an AR corepressor. As Ebp1 is decreased in preclinical models of hormone refractory prostate cancer, we studied the ability of Ebp1 to mitigate the hormone refractory phenotype. As we previously found that Ebp1 affected the expression of some androgen receptor target genes, we sought to determine a full spectrum of genes changed using an unbiased appraoch by microarry analysis. Experiment Overall Design: A hormone independent cell line C81 was derived from LNCaP cells by long term passage and was a kind gift of Dr. Lin (University of Nebraska). C81 cell were transfected with a vector control or EBP1 expression plasmids and mass cultures selected. RNA was collected from logaritmically growing cultures.
2008-11-13 | E-GEOD-12200 | biostudies-arrayexpress
Project description:Genome-wide mapping of the TSS in root and shoot from two maize lines B73 and Mo17 Genome-wide locations and dynamics of maize core promoters obtained from the experimental establishment of the TSSs coordinates. The work derived from this data it is the first genome-wide atlas of core promoters and its dynamic generated for an important crop species. Four samples each one with biological replicates. Comparisons were done between B73 and Mo17 for each of the tissues and between tissues for each line
2015-11-04 | E-GEOD-70251 | biostudies-arrayexpress
Project description:We report the effects of 1,25(OH)2D3 treatment on the microRNA expression in human muscle cells Primary cultures of human muscle cells were treated with 1,25(OH)2D3 or vehicle for 48 hours.
2015-11-24 | E-GEOD-70933 | biostudies-arrayexpress