Project description:Understanding the impact of DNA methylation within different disease contexts often requires accurate assessment of these modifications in a genome-wide fashion. Frequently, patient-derived tissue stored in long-term hospital tissue banks have been preserved using formalin-fixation paraffin-embedding (FFPE). While these samples can comprise valuable resources for studying disease, the fixation process ultimately compromises the DNA’s integrity and leads to degradation. Degraded DNA can complicate CpG methylome profiling using traditional techniques, particularly when performing methylation sensitive restriction enzyme sequencing (MRE-seq), yielding high backgrounds and resulting in lowered library complexity. Here, we provide results using our new MRE-seq protocol (Capture MRE-seq), tailored to preserving unmethylated CpG information when using samples with highly degraded DNA. The results using Capture MRE-seq correlate well (0.92) with traditional MRE-seq calls when profiling non-degraded samples, and can recover unmethylated regions in highly degraded samples when traditional MRE-seq fails, which we validate using bisulfite sequencing-based data (WGBS) as well as methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq).
Project description:We have identified a MORC3-regulated DNA element (MRE) that regulates the activation of IFNB1 upon loss of MORC3. To study the global transcriptional effects of the MRE, we deleted the MRE in STAT1–/– STAT2–/– and STAT1–/– STAT2–/– MORC3–/– BLaER1 monocytes and performed RNA-seq.
Project description:Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). E14 Day0 data for MRE-seq and MeDIP-seq are released first in previous publication and included in prior series GSE36114 ChIP-seq, 5-hmC-seq, MeDIP-Seq, MRE-Seq, ncRNA-Seq, and RNA-seq on activin-induced differentiating ES cells at 3 time points.
Project description:We generated two types 5-methylcytosine (5-mC) data in E14 mouse embryonic stem cells, using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq).