Project description:RNA-seq analysis (proinflammatory cocktail vs. control) of total RNA isolated from patient-derived colon organoids established from an ulcerative colitis patient. The analysis aimed at characterizing the epithelial gene expression changes post proinflammatory stimulation. ***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data
Project description:RNA-seq analysis of total RNA isolated from patient-derived organoids established from eight individuals. The organoids are genotyped with regards to rs2910686. The analysis aimed at characterizing the epithelial gene expression changes in ERAP2 proficient vs. ERAP2 deficient patient-derived organoids. ***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data
Project description:This series represents the work described in the publication Bacillus subtilis Genome Diversity by Earl et al. (Journal of Bacteriology, accepted) Keywords: comparative genomic hybridization
Project description:Purpose: The goal of this study was to use deep sequencing to identify all splice variants of Calcium/calmodulin-dependent kinase II (CaMKII) expressed in the human hippocampus. Methods: Transcripts of CaMKII-encoding genes (CAMK2A, CAMK2B, CAMK2G, and CAMK2D) were sub-amplified by PCR from total RNA extracted from human hippocampal tissue samples from 3 donors. Illumina sequencing libraries were constructed by PCR from these initial pools of amplicons and sequenced on an Illumina MiSeq instrument. Sequencing reads passing quality controls were clustered on the basis of sequence identity or near-identity. Consensus sequences of clusters were mapped with known exons of CaMKII genes to identify the splice variant represented by each cluster. Donor 1 replicate 2, Donor 2, and Donor 3 libraries from genes CAMK2B, CAMK2G, and CAMK2D were first sequenced on a MiSeq Nano flow cell, then re-pooled for read balancing and sequenced again of a full-size MiSeq flow cell. For each library, reads from Nano and full-size flow cells were combined for subsequent analysis. Results: We perfomed the first comprehensive survey of CaMKII transcripts expressed in individual tissue samples (human hippocampus). We detected a total of 79 splice variants of the four human CaMKIIs: CaMKIIα (3), CaMKIIβ (30), CaMKIIγ (24), and CaMKIIδ (22), across tissue samples from 3 donors. This represents the vast majority of possible in-frame CaMKII splice variants (Sloutsky and Stratton, European Journal of Neuroscience, 2020; https://doi.org/10.1111/ejn.14761).
Project description:This series represent the data set belonging to the publication by de Vries et al. Diagnostic genome profiling in mental retardation. American Journal of Human Genetics, vol 77: 606-616 (2005). In this study 100 patients with unexplained mental retardation were analyzed for DNA copy-number changes using a tiling-resolution genomewide microarray containing 32,447 BACs. Keywords: CGH
Project description:Calcium/calmodulin-dependent protein kinase II (CaMKII) was suggested to mediate ischemic myocardial injury and adverse cardiac remodeling. However, the specific functions of the CaMKII isoforms and splice variants in ischemia/reperfusion (I/R) injury have not been investigated yet. Thus, we studied the roles of the CaMKII isoforms and splice variants in I/R by the use of various CaMKII mutant mice. CaMKIIδC was up-regulated already one day after I/R injury but surprisingly, acute I/R injury was neither affected in CaMKIIδ-deficient mice, CaMKIIδ-deficient mice in which the splice variants CaMKIIδB and C were re-expressed nor in conditional CaMKIIδ/γ double-knockout mice (DKO). In contrast, 5 weeks after I/R, DKO mice were protected against extensive scar formation and cardiac dysfunction. Leukocyte infiltration was not altered one day but five days after I/R, explaining the late effects of CaMKII deletion on post-I/R remodeling. Other than reported before, we demonstrate that CaMKII is not critically involved in the immediate mechanisms that regulate acute I/R injury but in the process of post-infarct remodeling. We analysed 6 groups in total: 3 groups from wild-type control animals and 3 groups from CaMKII delta/gamma double-KO mice. Sham operated animals served as controls in both wild-type and KO animal groups. 2 different time points in ischia/reperfusion operated animals were investigated: 1 day and 5 days post-surgery.
Project description:Calcium/calmodulin-dependent protein kinase II (CaMKII) was suggested to mediate ischemic myocardial injury and adverse cardiac remodeling. However, the specific functions of the CaMKII isoforms and splice variants in ischemia/reperfusion (I/R) injury have not been investigated yet. Thus, we studied the roles of the CaMKII isoforms and splice variants in I/R by the use of various CaMKII mutant mice. CaMKIIδC was up-regulated already one day after I/R injury but surprisingly, acute I/R injury was neither affected in CaMKIIδ-deficient mice, CaMKIIδ-deficient mice in which the splice variants CaMKIIδB and C were re-expressed nor in conditional CaMKIIδ/γ double-knockout mice (DKO). In contrast, 5 weeks after I/R, DKO mice were protected against extensive scar formation and cardiac dysfunction. Leukocyte infiltration was not altered one day but five days after I/R, explaining the late effects of CaMKII deletion on post-I/R remodeling. Other than reported before, we demonstrate that CaMKII is not critically involved in the immediate mechanisms that regulate acute I/R injury but in the process of post-infarct remodeling.
Project description:Effect of NF-kB inhibition and activation on gene expression in mouse and human lung cancer cell-lines. Publication reference: Hopewell, E.L., Zhao, W., Fulp, W.J., Bronk, C.C., Lopez, A.S., Massengill, M., Antonia, S., Celis, E., Haura, E.B., Enkemann, S.A., Chen, D.T., and Beg, A.A. 2013. Lung tumor NF-kappaB signaling promotes T cell-mediated immune surveillance. The Journal of clinical investigation 123:2509-2522.
Project description:Deatails of the series are available in the publications Suzuki et al., The Journal of Bacteriology “Global gene expression analysis of iron-inducible genes in Magnetospirillum magneticum AMB-1”, accepted for the publication. The gene expression profiles were categorized into 5 patterns. Abstract of the publication: "feo, tpd and ftr which encode ferrous transporters were up-regulated under iron-rich conditions.The concomitant rapid iron uptake and magnetite formation suggest that these uptake systems serve as iron supply lines for magnetosome synthesis." Keywords: iron response
Project description:The CHIP-seq methods were used to determine the binding of cyclin D1 to mouse genomic DNA. The detailed description of this dataset can be found in the publication "ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice" in Journal of Clinical Investigation (https://www.jci.org/articles/view/60256).