Project description:This SuperSeries is composed of the following subset Series: GSE25083: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: normal head and neck tissue GSE25089: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: HNSCC GSE25091: Global hypomethylation identifies loci targeted for hypermethylation in head and neck cancer: blood controls Refer to individual Series
Project description:The aim of this experiment was to profile DNase-I accessibility at a subset of genomic regions in extremely high coverage. After DNase-I treatment, DNA fragments from specific loci were targeted using bead capture, amplified, and sequenced.
Project description:HEK293T/17 cells were genetically edited by SMART editing to assess the effectiveness of SMART editing. There are 4 target genes: CXCR4, Lmnb1, Nrl and NRXN3. Cultured cells were first synchronized at the G2/M phase. Then, cells were transfected with Cas9 RNP along with SMART or traditional templates. After culture for two to three days, cells were harvested, and genomic DNA was extracted. The targeted loci were amplified by PCR and sequenced on an Illumina MiSeq.
