Project description:Trophoblast stem cells lack MAP3K4 activity (TSKI4 cells) switch from epithelial phenotype to intermediate phenotype. Loss of epithelial phenotype is due to the loss of CBP histone acetyltransferase activity and the gain of histone deacetylase HDAC6 expression and activity. In our work, we identify a small network of 183 genes whose expression is co-regulated by MAP3K4, CBP, and HDAC6. Further, we define the key role of one of these co-regulated genes, Rel, in inducing epithelial phenotype in intermediate TSKI4 cells.
Project description:Two lines of Trypanosoma brucei were isolated from cattle in Uganda. The DNA is from parasites that had undergone two rodent passages.
Project description:Generation of single cell and single nuclei transcriptomic data of post-mortem tissues from a Malawi cohort. We aim to explore differences in the immune response between Covid-19, Non-Covid19 LRTD (lower respiratory tract disease) and no-LTRD at the single cell level from lung, nasal and blood. Autopsies were conducted through minimally invasive autopsy using needle-biopsy. Samples were then processed with a 10X Chromium in Blantyre, Malawi. Some samples were run individually and others pooled. Pooled samples were split using single nucleotide polymorphisms or through hashtag oligonucelotides. Data processing and analysis was performed in R using the Seurat package.
Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=183) when we compared gene expression in untreated MS patients (n=27) to IFN treated patients (n=48).
Project description:The present dataset ("dataset 3") is a subset of a large metastudy on AML classfication. It contains normalized gene expression values of 1181 samples. In total, three datasets were generated, each containing data of a different platforms: dataset 1 (Affymetrix HG-U133 A microarrays), dataset 2 (Affymetrix HG-U133 2.0 microarrays) and dataset 3 (RNA-seq). Dataset 3 was generated using the following strategy: All data sets published in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) on 20 September 2017 were reviewed for inclusion in the present study. Basic criteria for inclusion were the cell type under study (human peripheral blood mononuclear cells (PMBCs) and/or bone marrow samples) as well as the species (Homo sapiens). Furthermore, GEO SuperSeries were excluded to avoid duplicated samples. We filtered the datasets for data generated with high-throughput RNA sequencing (RNA-seq) and excluded studies with very small sample sizes (< 10 samples). We then applied a disease-specific search, in which we filtered for acute myeloid leukemia, other leukemia and healthy or non-leukemia-related samples. The results of this search strategy were then internally reviewed and data were excluded based on the following criteria: (i) exclusion of duplicated samples, (ii) exclusion of studies that sorted single cell types (e.g. T cells or B cells) prior to gene expression profiling, (iii) exclusion of studies with inaccessible data. Other than that, no studies were excluded from our analysis. In total, the datasets contained samples from the following GSE Series: GSE63085, GSE32874, GSE58335, GSE86884, GSE63703, GSE63646, GSE63816, GSE72790, GSE81259, GSE85712, GSE45735, GSE64655, GSE87186, GSE49642, GSE52656, GSE62190, GSE66917, GSE67039, GSE61162, GSE67184, GSE49601, GSE78785, GSE79970. All raw data files were downloaded from GEO. Transcript abundances were calculated using kallisto version 0.43.0 and all data was normalized with the R package DESeq2 (R version R-3.2.4, DESeq2 version 1.12.4) with standard parameters. Genome build hg38 was used for read alignment. No filtering of low-expressed genes was performed.
Project description:MYCN is a master regulator controlling many processes necessary for tumor cell survival. Here, we unravel a microRNA network that causes tumor suppressive effects in MYCN-amplified neuroblastoma cells. In profiling studies, histone deacetylase (HDAC) inhibitor treatment most strongly induced miR-183. Enforced miR-183 expression triggered apoptosis, and inhibited anchorage-independent colony formation in vitro and xenograft growth in mice. Furthermore, the mechanism of miR-183 induction was found to contribute to the cell death phenotype induced by HDAC inhibitors. Experiments to identify the HDAC(s) involved in miR-183 transcriptional regulation showed that HDAC2 depletion induced miR-183. HDAC2 overexpression reduced miR-183 levels and counteracted the induction caused by HDAC2 depletion or HDAC inhibitor treatment. MYCN was found to recruit HDAC2 in the same complexes to the miR-183 promoter, and HDAC2 depletion enhanced promoter-associated histone H4 pan-acetylation, suggesting epigenetic changes preceded transcriptional activation. These data reveal miR-183 tumor suppressive properties in neuroblastoma that are jointly repressed by MYCN and HDAC2, and suggest a novel way to bypass MYCN function.
Project description:Anopheles gambiae isofemale families from Tororo, Uganda were assayed for resistance to lambda-cyhalothrin (1.5hr exposure). Resistant families were compared to susceptible families. A portion of each family was exposed to 0.05% lambda-cyhalothrin in order to determine the family phenotype. The families used for the array were of known phenotype but were themselves unexposed.
Project description:We used whole genome expression profiling to analyze the effects of Zika virus (ZIKV) strains Uganda and French Polynesia on the mRNA transcriptome of induced pluripotent stem cell-derived human neural stem cells (long-term self-renewing neuroepithelial-like stem (lt-NES®) cells) - particularly to identify differentially expressed genes which are associated with microcephaly phenotype.