The most common oncogenic mutations in multiple myeloma (MM) affect N- and K-RAS leading to constitutive activation of RAS-dependent signaling. Signal transduction via RAS, Raf and MAPK has been well described as a canonical pathway. In accordance with this assumption, we showed that the activity of the MEK/ERK module is strictly dependent on pan-Raf activity. However, inhibition of MEK/ERK has no or only minor effects on MM cell survival, whereas oncogenic Ras and pan-Raf critically contribute to survival of multiple myeloma cells. Therefore, we aimed to learn more about Raf-dependent but MEK-independent signaling effectors.
Pan-Raf co-operates with PI3K-dependent signalling and critically contributes to myeloma cell survival independently of mutated RAS.
Cell line
View SamplesTo estimate mRNA steady-state levels we used RNA extracted from logarithmically growing fisson yeast cells on Affymetrix Yeast 2.0 Genechip arrays. The signal intensities from two independent biological repeats were averaged, resulting in measurements for 4818 out of 4962 nuclear protein-coding genes.
A network of multiple regulatory layers shapes gene expression in fission yeast.
Sex, Subject
View SamplesTo define the molecular regulators of metastasis of triple-negative breast cancer, we conducted a rigorous characterization of four isogenic populations of MDA-MB-231 human triple-negative breast cancer cells that display a range of intrinsic spontaneous metastatic capacities in immuno-deficient mice, from non-metastatic to highly metastatic to lung, liver, spleen and spine. PAT-Seq gene expression profiling of primary tumor cells identified the fibroblast growth factor homologous factor, FGF13, as a candidate metastatic virulence gene highly upregulated in aggressively metastatic MDA-MB-231HM tumors. Overall design: Gene expression analysis from PAT-Seq of 4 increasingly metastatic breast cancer xenograft tumours
Functional and genomic characterisation of a xenograft model system for the study of metastasis in triple-negative breast cancer.
Specimen part, Subject
View SamplesRNA seqeuncing was performed to identifiy changes in genes expression and alternative splicing following SRSF3 depletion in pluripotent stem cells. Overall design: Induced pluripotent stem cells (iPSCs) generated from reprogrammable conditional SRSF3 knockout (SRSF3-KO/OKSM) mouse embryonic fibroblasts (MEFs) were induced for 24h to deplete SRSF3 and RNA seqeuncing was performed.
SRSF3 promotes pluripotency through <i>Nanog</i> mRNA export and coordination of the pluripotency gene expression program.
Specimen part, Subject
View SamplesThe PAT-seq approach was utilised to determine the gene expression changes over the cell-cycle of wildtype and delta-set1 yeast strains. The cell were synchronised by alpha-factor arrest and cell-cycle release Overall design: Analysis gene expresson across the S. cerevisiae cell cycle.
Coordination of Cell Cycle Progression and Mitotic Spindle Assembly Involves Histone H3 Lysine 4 Methylation by Set1/COMPASS.
Cell line, Subject, Time
View SamplesThis SuperSeries is composed of the SubSeries listed below.
Production of BMP4 by endothelial cells is crucial for endogenous thymic regeneration.
Sex, Specimen part
View SamplesThe thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.
Production of BMP4 by endothelial cells is crucial for endogenous thymic regeneration.
Sex, Specimen part
View SamplesThe thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.
Production of BMP4 by endothelial cells is crucial for endogenous thymic regeneration.
Sex, Specimen part
View SamplesBacteria selectively consume some carbon sources over others through a regulatory mechanism termed catabolite repression. Here, we show that the base pairing RNA Spot 42 plays a broad role in catabolite repression in Escherichia coli by directly repressing genes involved in central and secondary metabolism, redox balancing, and the consumption of diverse non-preferred carbon sources. Many of the genes repressed by Spot 42 are transcriptionally activated by the global regulator CRP. Since CRP represses Spot 42, these regulators participate in a specific regulatory circuit called a multi-output feedforward loop. We found that this loop can reduce leaky expression of target genes in the presence of glucose and can maintain repression of target genes under changing nutrient conditions. Our results suggest that base pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression.
The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli.
Specimen part
View SamplesIn order to gain insight into relative stability of transcripts in plants that lacked m6A, we performed global mapping of uncapped and cleaved transcripts Overall design: 2 replicates of GMUCT in Arabidopsis thaliana ecotype Col-0 ABI3:MTA (mta) plants. genome-wide mapping of uncapped and cleaved transcripts (GMUCT)
N<sup>6</sup>-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis.
Specimen part, Subject
View Samples