Project description:DNA methylation is a key component of the mammalian epigenome, playing a regulatory role in development, disease, and other processes. Robust, high-throughput single-cell DNA methylation assays are now possible (sciMET); however, the genome-wide nature of DNA methylation results in a high sequencing burden per cell. Here, we leverage target enrichment with sciMET to capture sufficient information per cell for cell type assignment using substantially fewer sequence reads (sciMET-cap). Sufficient off-target coverage further enables the production of near-complete methylomes for individual cell types. We characterize sciMET-cap on human PBMCs and brain (middle frontal gyrus).
Project description:The goal of this experiment was to identify transcripts that are differentially expressed in CAP-D3 and CAP-H2 depleted cells with and without exposure to menadione
Project description:Transcriptome analysis of two different mutants of the condensin II subunit CAP-D3. Four week-old plantlets from the T-DNA insertion lines SAIL_826_B06 (cap-d3 SAIL) and SALK_094776 (cap-d3 SALK) were compared to Col-0 wild-type plants.
Project description:The mRNA cap recruits factors essential for transcript processing and translation initiation. We report that regulated mRNA cap methylation is a feature of embryonic stem cell (ESC) differentiation. Expression of the mRNA cap methyltransferase activating subunit, RAM, is elevated in ESCs resulting in high levels of mRNA cap methylation and expression of Oct4 and Sox2 and other pluripotency-associated factors. During neural differentiation, RAM is suppressed which is required for loss of Oct4 and Sox2 and correct expression of neural markers. Cells were treated with control or RAM siRNA and cytosolic RNA or polysome RNA (actively translated) was sequenced.
Project description:The mRNA cap recruits factors essential for transcript processing and translation initiation. We report that regulated mRNA cap methylation is a feature of embryonic stem cell (ESC) differentiation. Expression of the mRNA cap methyltransferase activating subunit, RAM, is elevated in ESCs resulting in high levels of mRNA cap methylation and expression of Oct4 and Sox2 and other pluripotency-associated factors. During neural differentiation, RAM is suppressed which is required for loss of Oct4 and Sox2 and correct expression of neural markers.
Project description:Protocol Title: Three Arm Prospective Randomized controlled trial of High-Definition White-light colonoscopy versus High-Definition White-light colonoscopy with Reveal Distal Attachment Cap versus High-Definition White-light colonoscopy with Endocuff Vision for the detection of colorectal adenomas
Hypothesis: Detection rate of adenomas in patients will be higher in procedures performed with High-Definition White-light (HDWL) colonoscopy with Reveal distal attachment cap and HDWL colonoscopy with Endocuff Vision compared to HDWL colonoscopes alone
Design: Multicenter, Prospective, randomized controlled study
Primary Aim: To compare the proportion of subjects with at least one adenoma detected during HDWL colonoscopy versus HDWL colonoscopy with Reveal distal attachment cap versus HDWL colonoscopy with Endocuff Vision.
Secondary Aims: To compare the number of adenomas detected per subject with HDWL colonoscopy versus HDWL colonoscopy with Reveal distal attachment cap versus HDWL colonoscopy with Endocuff Vision.
To compare the detection rates for polyp subtypes (including advanced adenomas, serrated polyps, right sided adenomas, etc.), cecal intubation rate, insertion time, withdrawal time, and complications of HDWL colonoscopy versus HDWL colonoscopy with Reveal distal attachment cap versus HDWL colonoscopy with Endocuff Vision.
