Project description:Somatic STAT5B gain-of-function mutations have been frequently found in patients with T- and NK-cell neoplasms. STAT5BN642H represents the most frequently occuring STAT5B mutation. To investigate the molecular mechanism of STAT5BN642H-driven NK-cell leukemia, we performed RNA-Seq of liver derived FACS-sorted diseased N642HNK/NK and aged non-diseased control (Cre neg, GFPNK/NK), STAT5BNK/NK, N642HNK/NK NK cells.
Project description:This experiment was perfomed to understand the role of Cyclin C in BCR-ABL1 driven leukemia. Bone marrow from mice harbouring a homozygous Cyclin C knock-out as well as from wild type control mice was transduced with a BCR-ABL1 expressing retrovirus to generate stable cell lines. Cells were harvested for RNA seq from in-vitro cultures of these cell lines (\\"in-vitro\\" samples). 500000 cells of the same cultures were injected into the tail vains of NSG mice. After 10 days the cells were isolated from the bone marrow of the recipient mice and collected for RNA sequencing (\\"ex-vivo\\" samples). Library prep and sequencing was perfomed for in-vitro and ex-vivo samples together.
Project description:Single-embryo SMART-seq2 of mouse 2-cell stage embryos. The embryos have been generated with in vitro fertilization (IVF) and are staged as hours post-IVF.
Project description:Cardiac remodelling is a key process in the development of heart failure. Reactivation of foetal cardiac genes is often associated with cardiac remodelling, which might be the result of the activation of signalling pathways involved in heart failure. Here we studied the role of Pontin (Ruvbl1), which is highly expressed in embryonic hearts, in mediating adverse remodelling in adult mouse hearts.
Project description:This experiment was performed to elucidate the effects of CDK6 on CALR-mutant Myeloproliferative Neoplasms. VavCre CALRdel52 knockin mice were crossed with full-body Cdk6-/- mice to obtain Cdk6-/- CALRdel52 mice. Bone marrow from mice of the four genotypes Cdk6+/+ CALR+/+ (wild-type), Cdk6+/+ CALRdel52 (CALR-mutant), Cdk6-/- CALR+/+ (Cdk6 knockout) and Cdk6-/- CALRdel52 (CALR-mutant with Cdk6 knockout) was isolated and stained for flow cytometry. To obtain megakaryocyte progenitors (MkPs) from the bone marrow, Lineage (CD11b, Gr-1, Ter119, CD3, CD19), c-Kit, sca-1, CD150 and CD41 surface markers were used. From the gating strategy: Lineage- c-Kit+ sca-1- CD150+ CD41+, MkPs were sorted into round-bottom collection tubes via fluorescence activated cell sorting (FACS). These cells were then used for RNA-isolation and subsequent RNA-Sequencing. The samples were harvested in two batches (Sample dates: \"February\" and \"April\").
Project description:To explore transcriptional similarities between human and murine Anaplastic Large Cell Lymphoma (ALCL) cell lines, RNA sequencing was performed across both species. The human cell lines included SU-DHL-1, DEL, SUP-M2, Karpas-299, SR-786, Mac1 and Mac2a. Additionally, murine cell lines derived from tumors with distinct genetic backgrounds (NPM-ALK(Tg/+), NPM-ALK(Tg/+)Cdk6-/- and NPM-ALK(Tg/+)Stat5b-/-) were analyzed to identify gene expression differences associated with tumor development in the absence of CDK6 or STAT5B.
Project description:To investigate direct genomic targets of CDK6 and STAT5B in Anaplastic Large Cell Lymphoma (ALCL), ChIP-sequencing (ChIP-seq) was performed in both human and murine ALCL cell lines. We performed ChIP targeting STAT5B in five human ALCL cell lines (SU-DHL-1, DEL, SUP-M2, Karpas-299, SR-786) and ChIP targeting CDK6 in one murine ALCL cell line derived from a NPM-ALK(Tg/+) mouse.
Project description:The kidney contains distinct glomerular and tubulointerstitial compartments with diverse cell types and extracellular matrix components. Glomerular disease is characterized by excess matrix deposition and the loss of filtration barrier integrity. The role of immune cells in glomerular disease is crucial for dampening inflammation and maintaining homeostasis. Macrophages are innate immune cells influenced by their tissue microenvironment, but it is unclear how these cells contribute to distinct extracellular matrix compartments within the kidney. Bulk RNA-sequencing was used to determine the transcriptional landscapes of kidney macrophages.
Project description:In vitro studies have been invaluable in unravelling the complexity of the core clock mechanism and their responses to various stimuli. However, fidelity of in vitro cell culture as a proxy for studying tissue and cell type specific rhythmic processes in vivo has not been rigorously tested. This study compared the rhythmic transcriptomes between chondrocytes synchronised in vitro with three methods and in vivo cartilage rhythmic transcriptome. Using high-throughput RNA-sequencing of primary chondrocytes synchronized via heat shock, dexamethasone, and osmotic stress, we demonstrate that while all three methods robustly induce circadian rhythms in the expression of the core clock genes, each method results in distinct rhythmic transcriptome with little overlap.