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Expression data from wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

ABSTRACT: WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours. Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription Keywords: comparative study

ORGANISM(S): Mus musculus

PROVIDER: GSE6837 | GEO | 2007/01/31

SECONDARY ACCESSION(S): PRJNA99169

REPOSITORIES: GEO

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Transcription profiling of mouse wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

Project description:WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours. Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription Experiment Overall Design: WT and Ikbke cells were either stimulated and left untreated to compare their response to interferon.

2008-06-15 | E-GEOD-6837 | biostudies-arrayexpress

IKKe coordinates invasion and metastasis

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IKKe coordinates invasion and metastasis

Project description:IKKe was identified previously as a breast cancer oncogene and was associated with poor clinical outcome in ovarian cancer. In order to elucidate functional roles of IKKe, we used microarray analysis to identify genes changed upon IKKe shRNA knockdown and compared with genes affected in ovarian cancers IKKe was knockdowned by 2 different IKKe shRNAs in Ovcar5 in 6 replicates and candidate downstream targets were selected if changed by both shRNAs

2012-11-16 | E-GEOD-42320 | biostudies-arrayexpress

Mus musculus

Project description:Expression data from wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF)

| PRJNA99169 | ENA

RNA-seq based characterization of long non-coding RNA involved in respiratory viruses pathogenesis

Project description:This dataset includes both whole transcriptome (WT) and mRNA-seq data for interferon-treated mouse samples. This is part of a larger study (GSE52405), where these interferon datasets were used as validation. 6-week-old C57BL/6J mice were treated with 10,000 U of recombinant interferon (Universal Type I IFN, Recombinant Human IFN-alpha A/D [BglII], R&D Systems) dissolved in endotoxin-free phosphate-buffered saline (EF-PBS), or with EF-PBS alone. For this study, the mice at 12 hours post-treatment were used.

2014-05-27 | E-GEOD-55480 | biostudies-arrayexpress

Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [Ribosome Profiling]

Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.

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Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P [RNA sequencing]

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Comparison between MCF7-IKKe overexpressing cells and MCF7 control cells

Project description:Analysis of differentially expressed genes in MCF7 cancer cells transiently transfected with an expression vector containing the ORF of IKKe and as a control, cells were transfected with a vector containing the ORF of Lacz.

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Ef-cd locus shortens rice maturity duration without yield penalty

Project description:The contradiction between ‘high-yielding’ and ‘early-maturing’ hampers further improvement on annual rice yield. Here we reported the positional cloning of a major maturity duration-regulatory gene, Early flowering-completely dominant (Ef-cd), and demonstrated that natural variation in Ef-cd could be used to overcome the above contradictory. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition. Field test comparisons of early-maturing Ef-cd near-isogenic lines (NILs) with their wild types as well as the derivative early-maturing hybrids with their wild-type hybrids conducted under different latitudes determined that early-maturing Ef-cd allele shortens maturity duration (ranging from 7 to 20 days) without a concomitant yield penalty. Ef-cd facilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessing Ef-cd matured significantly earlier. Therefore, Ef-cd could be a vital contributor of elite early-maturing hybrid varieties in balancing grain yield with maturity duration.

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2022-05-08 | GSE202367 | GEO

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