Project description:ProB-PreB, immature and mature B cells were sorted from the bone marrow of mice and the RNA subsequently sequenced. The mice were all Mb1-Cre +/- and either Vhl flox/flox or VHL flox/WT
Project description:Total RNA was isolated from pre BI (early lymphcytes) cells sorted by FACS with the following markers: B220+, CD25-, C-kit+,IgM-, CD19+. The animals used carried floxed Hdac1 & 2 either in combination with mb1-cre (refered to as DKO) or not (WT).
Project description:To unravel the potential cooperative roles of oxygen-regulated signaling pathways; von Hippel-Lindau (VHL) tumor suppressor protein and hypoxia-inducible factor (HIF) transcription factors, we have generated mutant mice with; Vhlh, Vhlh/Hif1α, Vhlh/Hif2α and Vhlh/Hif1α/Hif2α gene alleles floxed. Subsequently primary kidney cells were isolated, cultured and infected with Adenoviruses bearing either Cre/GFP or GFP expression only. Agilent cDNA microarrays were utilized to compare the gene expression profiles of the kidney epithelial cells from aforementioned cell cultures to gain insight about the molecules and signaling pathways that drive aberrant cellular proliferation in clear cell renal cell carcinoma (ccRCC).
Project description:To examine the transcriptional changes that occur following alpha4 deletion, RNA microarray analysis was performed using RNA from alpha4-floxed MEFs 48 hours after infection with the Cre-containing or Vector control virus. Keywords: other
Project description:Total RNA was isolated from pre BI (early lymphcytes) cells sorted by FACS with the following markers: B220+, CD25-, C-kit+,IgM-, CD19+. The animals used carried floxed Hdac1 & 2 either in combination with mb1-cre (refered to as DKO) or not (WT). 6 samples of FACS-sorted pre BI cells were analyzed, corresponding to 6 individual female animals, 8 week of age, 3 per genotype DKO and WT.
Project description:The transcriptomic impact of Hells loss-of-function was quantified by RNA sequencing of sample from conditional knockout (Mb1-Cre+/WT HellsF/F) and littermate control mice (Mb1-CreWT/WT HellsF/F). Three time points were chosen to follow the kinetic: day 0 for naïve B cells collection, day 7 and day 14 post NP-CGG intraperitoneal immunization for germinal center B cells collection. At each time point, 4 mice of each genotype were used. Live cells were FACS sorted (AriaIII) using surface markers as follows: B220+CD21+CD23+ for naïve B cells, and B220+CD95+GL7+ for germinal center B cells. Due to their low frequency, germinal center B cells were FACS-sorted twice using the same gating strategy. Collected samples were lysed and processed for RNA extraction.
Project description:To unravel the potential cooperative roles of oxygen-regulated signaling pathways; von Hippel-Lindau (VHL) tumor suppressor protein and hypoxia-inducible factor (HIF) transcription factors, we have generated mutant mice with; Vhlh, Vhlh/Hif1α, Vhlh/Hif2α and Vhlh/Hif1α/Hif2α gene alleles floxed. Subsequently primary kidney cells were isolated, cultured and infected with Adenoviruses bearing either Cre/GFP or GFP expression only. Agilent cDNA microarrays were utilized to compare the gene expression profiles of the kidney epithelial cells from aforementioned cell cultures to gain insight about the molecules and signaling pathways that drive aberrant cellular proliferation in clear cell renal cell carcinoma (ccRCC). 24 independent biological samples from 4 genetic experimental conditions were hybridized in two- color format on 13 Mouse GE 4x44K v2 Microarray Kit (Design ID 026655) arrays. Eventual dye specific hybridization effects were controlled with dye swap on biological replicates. For an each experimental condition 3 arrays were use, except of one where 4 arrays were used (one sample combination in repetition with a dye swap). For the final analysis the gene expression levels were dye effect corrected and values for biological replicates were averaged to obtain a matrix with gene expression levels for 4 independent biological (1. Vhlh-/-, 2. Vhlh-/-/Hif1α-/-, 3. Vhlh-/-/Hif2α-/- and 4. Vhlh-/-/Hif1α-/-/Hif2α-/-) conditions.
Project description:To determine why double deficiency of Vhl and Pbrm1 but not single deficiency of either gene resulted in ccRCC, we performed gene expression profiling of RNA isolated from renal cortices of 3-month-old WT, VhlF/FKsp-Cre, Pbrm1F/FKsp-Cre, and VhlF/FPbrm1F/FKsp-Cre mice.
Project description:Purpose: We compared the transcriptomes of mouse CD4 T cells lacking the vhl gene ( vhlfl/fl cd4 cre= vhl cKO) with WT controls from the lungs of mice 8 weeks after aerosol infection with Mycobacterium tuberculosis. Results: Using an optimized data analysis workflow, between 40-55 million sequence reads per sample to the mouse genome (build mm10) and identified 14700 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: The transcriptome of WT anf vhl cKO was compared. Groups did cluster differentially with regards to their transcript abundance. The WT group has enriched DNA synthesis/ proliferation pathways whereas the Vhl cKO was enriched in hypoxia pathways. Transcripts assocaited with T cell differentiation were increased in WT group while T cell inhibitory molecules was elevated in the transcriptome of vhl cKO CD4 T cells.