Project description:Polycystic Kidney Disease (PKD) is a genetic disease of the kidney characterized by the gradual replacement of normal kidney parenchyma by fluid-filled cysts and fibrotic tissue. Autosomal Dominant Polycystic Kidney Disease (ADPKD) is caused by mutations in the PKD1 or PKD2 gene. Here we present an RNASeq experiment designed to investigate the effect of a kidney specific and Tamoxifen inducible knockout of the Pkd1 gene in mice. 7 mice were grouped into two groups, 4 Tamoxifen treated mice which develop an adult onset Polycystic Kidney Disease phenotype and 3 untreated mice which have WT phenotype.
Project description:MicroRNAs are important negative regulators of protein coding gene expression, and have been studied intensively over the last few years. To this purpose, different measurement platforms to determine their RNA abundance levels in biological samples have been developed. In this study, we have systematically compared 12 commercially available microRNA expression platforms by measuring an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples, and synthetic spikes from homologous microRNA family members. We developed novel quality metrics in order to objectively assess platform performance of very different technologies such as small RNA sequencing, RT-qPCR and (microarray) hybridization. We assessed reproducibility, sensitivity, quantitative performance, and specificity. The results indicate that each method has its strengths and weaknesses, which helps guiding informed selection of a quantitative microRNA gene expression platform in function of particular study goals.
Project description:In order to determine whether dis-regulation of a genetic pathway could explain the increased apoptosis of parp-2-/- double positive thymocytes, the gene expression profiles in double positive thymocytes derived from wild-type and parp-2-/- mice were analysed using Affymetrix oligonucleotide chips (mouse genome 430 2.0).
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:H. seropedicae wild-type or ntrC mutant were grown on three different nitrogen conditions: nitrogen limiting, ammonium shock and nitrate shock.
Project description:To evaluate the in vivo metastatic activity of five different melanoma cell lines (LCP, LCM, WM266, SKMel28 and A375), we completed intra-cardiac injection of 1x106 luminescent cells in NOD-SCID mice. All melanoma cell lines demonstrated a metastatic behaviour following intra-cardiac injection with a variable attitude to produce bone and visceral metastasis. Mice injected with LCP, LCM and WM266 showed a lower total metastatic tumor burden and increased survival (low metastatic) as compared to A375 and SK-Mel28 (high metastatic). Melanoma cell lines were profiled for gene expression (RNAseq) of 118 genes notably involved in cancer progression and metastasis.
Project description:According to our current knowledge, de novo glycerophospholipid (GPL) synthesis begins with the acylation of glycerol-3-phosphate to produce phosphatidic acid, the precursor of all other GPLs. Here we describe an alternative GPL synthesis pathway that starts with the acyl-CoA-dependent acylation of glycerophosphoglycerol (GPG), resulting in the formation of lysophosphatidylglycerol (LPG). The acyltransferase reaction is catalyzed by the Batten disease-associated protein ceroid lipofuscinosis neuronal 8 (CLN8). Tracer studies revealed that CLN8-derived LPG is selectively converted into bis(monoacylglycero)phosphate (BMP), a GPL essential for lysosomal lipid homeostasis, but not into phosphatidylglycerol and cardiolipin. CLN8-knockout cells and mice cannot utilize GPG for BMP synthesis, resulting in BMP-deficiency and excess accumulation of phospholipids in lysosomes. The lipid synthesis pathway described herein is relevant for understanding lysosomal lipid metabolism and the pathogenesis of neurodegenerative diseases.