Project description:The activity of PGR and H3K27ac in peri-ovulatory mouse granulosa cells was characterized using chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq)
Project description:Reads from massively parallel sequencing of RNA primed, short nascent strands from asynchronously growing cancer cells (K562, MCF7). Newly replicated DNA was isolated based on size (400-800 bp) and the presence of a short RNA stretch at the 5' end using lambda exonuclease. Purified nascent strands were analyzed using massively parallel sequencing. Sheared genomic DNA was sequenced as a control.
Project description:We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Identification of m6A modified sequences in HepG2 cells. HepG2 cells were incubated with either IFNg (200ng/ml) or HGF/SF (10 ng/ml) over night. Stress effects were tested in HepG2 cells by either 30 minutes incubation at 43M-BM-:C (heat shock) or UV irradiation of 0.04 J/cm2 followed by 4 hours of recovery in normal growing conditions prior to harvesting using Trypsin.
Project description:Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) was performed by using the anti-BPTF antibody in MGC803 cells to explore the downstream target genes of BPTF.
Project description:DNA methylation is a complex epigenetic marker that can be analysed using a wide variety of methods. Interpretation and visualisation of DNA methylation data can mask complexity in terms of methylation status at each CpG site, cellular heterogeneity of samples and allelic DNA methylation patterns within a given DNA strand. Bisulfite sequencing is considered the gold standard, however visualisation of massively parallel sequencing results remains a significant challenge. We created a program called Methpat that facilitates visualisation and interpretation of bisulfite sequencing data generated by massively parallel sequencing. To demonstrate this, we performed multiplex PCR that targeted 48 regions of interest across 95 human samples. The regions selected included known gene promoters associated with cancer, repetitive elements, known imprinted regions and mitochondrial genomic sequences. We interrogated a range of samples including human cell lines, primary tumours and primary tissue samples. Methpat generates two forms of output: a tab delimited text file for each sample that summarises DNA methylation patterns and their read counts for each amplicon and a HTML file that summarises this data visually. Methpat can be used with publicly available whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) datasets with sufficient read depths. Using Methpat, complex DNA methylation data derived from massively parallel sequencing can be summarised and visualised for biological interpretation. By accounting for allelic DNA methylation states and their abundance in a sample, Methpat can unmask the complexity of DNA methylation and reveal further biological insight in existing datasets. Multiplex bisulfite PCR and Next Generation sequencing of primary human samples and breast cancer cell lines.
Project description:This experiment is looking at the mutational signatures generated by engineered HRAS mutations by using whole genome sequence generated on massively parallel next generation sequencers.
