Project description:To investigate the chromatin binding patterns of wildtype SOX10 versus schwannoma-derived mutant isoforms, we established SVG-p12 cell lines stably expressing either FLAG epitope tagged wildtype SOX10 or two different mutant isoforms of SOX10. We then performed chromatin immunoprecipitation-DNA sequencing on these SVG-p12 cell lines stably transduced with wildtype or mutant SOX10 isoforms using an anti-FLAG epitope antibody.
Project description:Changes in alternative splicing in breast cancer cells expressing control, empty vector or Flag-tagged wild type RBM47 were analyzed using paired-end, 100bp RNAseq. Related data published together with these data are found in GSE53779 Triplicate RNAseq libraries were prepared from non-clonal brain metastatic breast cancer cells stably expressing empty-vector, and a clonal cell line (wt#10) expressing Flag-tagged, wild-type RBM47 under a doxycline-inducible promoter, both treated for three days with doxycycline to induce transgene expression
Project description:Study was conducted to understand the effect of the cancer associated H2BE76K mutation. Using CRISPR/Cas9 Knock-in cell lines expressing FLAG-tagged WT and E76K mutant H2B, we conducted gene expression profiling experiments and studied the effect of the H2BE76K mutation on H2B occupancy using CUT&RUN sequencing.
Project description:Changes in alternative splicing in breast cancer cells expressing control, empty vector or Flag-tagged wild type RBM47 were analyzed using paired-end, 100bp RNAseq. Related data published together with these data are found in GSE53779
Project description:NIPP1, an established interactor of protein phosphatase 1 (PP1), is implicated in PRC2-mediated regulation of gene expression. Here, we explore whether PP1 associated with NIPP1 is involved in NIPP1-mediated regulation of genes. Therefore, we generated Hela Tet-off (HTO) cell lines that stably and inducibly express a Flag-tagged version of wild-type NIPP1 (HTO-NIPP1wt) or mutant NIPP1 (HTO_NIPP1m). The latter mutant lacks the major PP1 binding site by two point mutations in the RVXF-motif, an established PP1 - binding motif. All cell lines were derived from the same parental HeLa Tet-Off (HTO-PT) cell line which expresses only tTA transactivator and is used as a control. The Flag fusions were only expressed in the absence of doxycyline and at levels that were up to twofold higher than that of endogenous NIPP1. We performed a gene expression profiling of the HTO cell lines, using Whole Human Genome Oligo microarrays from Agilent. A Paired SAM analysis identified 1365 genes with an altered expression (P < 0.01) between the Flag-NIPP1 and parental cell lines. Importantly, only 185 genes were differentially expressed (P<0.01) between the Flag-NIPP1m and parental cell lines. Even more strikingly, only 5% of the genes that were affected by the expression of Flag-NIPP1 also showed a significantly different expression in the Flag-NIPP1m cells. A similar small overlap was noted when the analysis was restricted to the 50 genes that were most upregulated or downregulated by the expression of Flag-NIPP1. Finally, scatter plot analysis revealed no significant correlation between the genes that were affected by the expression of Flag-NIPP1 or Flag-NIPP1m. Collectively, these data demonstrate that a moderate increase in the concentration of NIPP1 affects the expression of numerous genes by a mechanism that depends on associated PP1.
Project description:To examine the role of formation of a strong sink during leaf senescence, we compared the expression profile of the flag leaf of three different sterile mutant lines with fertile plants. The fertile and sterile lines showed basically similar expression profiles of flag leaves sampled at the same time. However, the fertile lines showed more rapid and enhanced change in transcriptome as compared to the sterile lines indicating that leaf senescence initiated independent of sink formation and is accelerated by sink formation.
