Project description:Genetically engineered mice (GEM) are essential tools for understanding gene function and disease modeling. Due to historical reasons, gene targeting was at first done in embryonic stem cells (ESC) derived from the 129 family of inbred strains, leading to mixed background or congenic mice when crossed with C57BL/6 mice. Depending on the number of backcrosses and breeding strategies genomic segments from 129-derived ESC can be introgressed into the C57BL/6 genome at different levels, establishing a unique genetic makeup that needs characterization in order to obtain valid conclusions of experiments using GEM models. We sequenced wild-type (WT), heterozygous (Het) and knockout (KO) mouse embryonic fibroblasts (MEFs) from a knockout model of Sall2 (Sato A. et al, Zinc finger protein sall2 is not essential for embryonic and kidney development. Mol Cell Biol 2003, 23:62-69) maintained in a mixed background between C57BL/6J and 129P2OlaHsd mice. We also treated these cells with doxorubicin, as a global perturbation of the gene expression. With this schema, we aimed to detect genetic introgression of 129 mice onto C57BL/6J, KO-ligated variants (the so-called congenic footprint) and potential modifier genes.
Project description:TICAM1 knockout and wild-type (TICAM1 knockout MEFs with restored TICAM1 expression) MEFs were treated by c-di-GMP or DMSO for 4 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. Changes in gene induction, especially of interferon-stimulated genes, between c-di-GMP and DMSO treated cells were examined.
Project description:TICAM1 knockout and wild-type (TICAM1 knockout MEFs with restored TICAM1 expression) MEFs were treated by c-di-GMP or DMSO for 4 hours. Total RNA was analyzed via Illumina Mouse Ref-8 V2. Changes in gene induction, especially of interferon-stimulated genes, between c-di-GMP and DMSO treated cells were examined. Total RNA from c-di-GMP or DMSO treated wild-type MEFs, c-di-GMP or DMSO treated TICAM1 knockout MEFs were analyzed. Gene expression was compared between c-di-GMP treated and DMSO treated samples.
Project description:Abl kinases, which are required for multiple cellular processes, including proliferation, apoptosis, adhesion, cell migration, and stress responses, widely participate in the regulation of gene transcription. To illustrate the role of Abl kinase in gene expression, the transcription of approximately 22,000 genes in wild-type (WT) and c-abl/arg knockout MEFs was detected using Affymetrix GeneChips (Mouse Genome 430 2.0).
Project description:We have used primary MEFs derived from wild type and E2F4 null mice growing asynchrounously in serum to generate a signature for E2F4 pathway activation. 10 wild type and 10 E2F4 null samples were each assayed using the Affymetrics Mouse Genome 430A 2.0 array. Keywords: Primary MEFs from wild type and E2F4 null mice
Project description:Comparison of gene expression in wild type and Wt1 (Wilms tumor suppressor gene 1) heterozygous knockout mice. Background: in Wt1+/- mice (MF1 strain) litter sizes are significantly smaller than in wild type animals. In addition, we observe retarded embryonic development of pre-implantation embryos that are still within the oviduct. By gene expression analysis we want to elucidate the molecular basis for these phenomena.
Project description:Histone acetylations are known to impact gene transcription. Here, we have attempted to examine the role of Leishmania donovani histone acetyltransferases HAT4 and HAT2 in regulating global gene expression. The transcriptome of HAT4-null promastigotes (Samples 2A, 2B) and HAT2-heterozygous knockout promastigotes (Samples 3A, 3B) have been compared with the transcriptome of wild-type Leishmania promastigotes (Samples 1A, 1B) and fold change in gene expression with respect to the control wild-type has been determined.