Project description:We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC). Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).
Project description:We report the application of an uscfDNA-oriented sequencing pipeline profiling the cell-free DNA populations in plasma. The uscfDNA sequencing pipeline include two uscfDNA-optimized extraction methods (QiaM and SPRI) and one control extraction method (QiaC). Final libraries are made with a single-stranded library prepartion kit. We generate genome-wide maps revealing the presence of an uscfDNA population (25-99bp) in addition to the mncfDNA (100-250bp).
Project description:We report the setup of a new method to map 5-hydroxymethylcytosine (5hmC) genome-wide at CpG resolution. The method combines selective chemical labeling by 5hmC b-glucosyltransferase and exonuclease digestion of the DNA molecules bound to streptavidin beads after biotinylation of the 5-glucosylmethylcytosines. Associated with a straightforward bioinformatic analysis, this new procedure provides a cost-effective and fast method for mapping 5hmC at high resolution.
Project description:The structural complexity of nucleosomes underlies their functional versatility. Here we report a new type of complexity – nucleosome fragility, manifested as high sensitivity to micrococcal nuclease, in contrast to the common presumption that nucleosomes are similar in resistance to MNase digestion. Using differential MNase digestion of chromatin and high-throughput sequencing, we have identified a special group of nucleosomes termed fragile nucleosomes throughout the yeast genome, nearly one thousand of which are at previously determined “nucleosome free” loci. Nucleosome fragility is broadly implicated in multiple chromatin processes, including transcription, translocation and replication, in correspondence to specific physiological states of cells. In the environmental-stress-response genes, the presence of fragile nucleosomes prior to the occurrence of environmental changes suggests that nucleosome fragility poises genes for swift up-regulation in response to the environmental changes. We propose that nucleosome fragility underscores distinct functional statuses of the chromatin and provides a new dimension for portraying the landscape of genome organization. Comparing nucleosome occupancy under different MNase digestion levels and growth conditions.
Project description:This experiment was performed to help optimize a digestion protocol for FACS of adult mouse lung cells. The sample JH2 was used to help generate lung epithelial cell signatures.
Project description:In this study we developed MPE-seq, a method for the genome-wide characterization of chromatin that involves the digestion of nuclei with methidiumpropyl-EDTA-Fe(II) [MPE-Fe(II)] followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. We also performed MNase-seq as a comparison. We further performed ChIP-seq using chromatin samples obtained by MPE-Fe(II) or MNase digestion of nuclei.