Project description:We performed a large-scale genome-wide characterisation of indels generated following editing with CRISPR/Cas9. We used pools of sgRNAs and performed targeted capture and sequencing of the edited regions in HepG2 cells.
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:Due to the large size, complex splicing and wide dynamic range of eukaryotic transcriptomes, RNA sequencing samples the majority of expressed genes infrequently, resulting in sparse sequencing coverage that can hinder robust isoform assembly and quantification. Targeted RNA sequencing addresses this challenge by using oligonucleotide probes to capture selected genes or regions of interest for focused sequencing. This enhanced sequencing coverage confers sensitive gene discovery, robust transcript assembly and accurate gene quantification. Here we describe a detailed protocol for all stages of targeted RNA sequencing, from initial probe design considerations, capture of targeted genes, to final assembly and quantification of captured transcripts. Initial probe design and final analysis can take less than a day, while the central experimental capture stage requires ~7 days.
Project description:To determine if random biopsies can be safely eliminated from screening of average risk persons with IBD, the investigators propose to carry out a pilot randomized control trial in which targeted biopsies in combination with random biopsies will be compared to targeted biopsies alone in terms of pre-cancerous lesion capture rate, side-effects and CRC risk. The pilot study will aim to capture 20% of the overall study population in order to evaluate the feasibility of recruiting the needed number of participants in the specified time frame, while maintaining high quality of data collection.
Project description:Multiplexed Chromatin Conformation Capture in Mouse Erythroid cells , from hundreds of targeted loci, using agilent oligo capture technology and high throughput sequencing.
