Project description:We report the application of chromatin immunoprecipitation and next generation sequencing technology for HIF1a binding sites at genome wide level in a RCC (renal cell carcinoma) cell line under hypoxia conditions. We found HIF1a binding sites in Caki-2 cell line under hypoxia conditions. Especially, we found HIF1a bind to SPOP under hypoxia condition, which was further validated. Examination of HIF1a binding sites in Caki-2 cell line under hypoxia condition
Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected. One mild digestion and one extensive digestion was applied to the mESC cells, followed by sequencing.
Project description:Micrococcal nuclease was used to digest mESC nuclei under a mild digestion condition to release the relatively open chromatin, and under an extensive digestion condition to release the genome chromatin. By comparing the genome distribution of mono-nucleasome under these two conditions, open chromatin regions were detected.
Project description:We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for M-OM-^C70 under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure" Examination of occupancy of FNR adn M-OM-^C70 under aerobic and anaerobic growth in conditions.
Project description:ATF4 is a stress-responsive gene which is critical for cell survival under stress conditions. ATF4 expression is upregulated under mitochondrial stress and the expression of a few chromatin remodelling genes are regulated by ATF4. ATAC-seq was performed on differentiated neurons after shATF4 knock-down under normal and mitochondrial stress conditions.
Project description:We used miRNA array to study differential expression of miRNA under hypoxia exposure in cancer cells. Cells cultured under normoxia were used as controls.
Project description:We report the application of chromatin immunoprecipitation and next generation sequencing technology for HIF1a binding sites at genome wide level in a RCC (renal cell carcinoma) cell line under hypoxia conditions. We found HIF1a binding sites in Caki-2 cell line under hypoxia conditions. Especially, we found HIF1a bind to SPOP under hypoxia condition, which was further validated.
Project description:This data set reveals the changes of histone modifications and chromatin accessibility in human umbilical vein endothelial cells (HUVECs) under atheroprotective pulsatile shear (PS), atheroprone oscillatory shear (OS), or with KLF4 overexpression. Using ChIP-Seq, we defined the H3K27ac and H3K4me1 enrichment under PS and OS conditions. Using ATAC-seq, we identified the chromatin accessibility under KLF4 overexpression.
Project description:This data set reveals the changes of histone modifications and chromatin accessibility in human umbilical vein endothelial cells (HUVECs) under atheroprotective pulsatile shear (PS), atheroprone oscillatory shear (OS), or with KLF4 overexpression. Using ChIP-Seq, we defined the H3K27ac and H3K4me1 enrichment under PS and OS conditions. Using ATAC-seq, we identified the chromatin accessibility under KLF4 overexpression.