Project description:To systematically analyzed the genome-wide characterization of potential eccDNAs in mouse heart tissues, we peformed Circle-seq in embryonic, neonatal and adult mouse heart tissues.
Project description:Adenosine base editing to recreate the HPFH mutations is a promising approach to induce HbF. We used CIRCLE-seq to identify 682 potential off-target sites in purified DNA treated with Cas9 nuclease complexed to sgRNA targeting -globin -175 .
Project description:We generated Circle-seq data for primary neuroblastoma to describe the landscape of extrachromosomal circular DNA in neuroblastoma.
Project description:We generated Circle-seq data for 12 neuroblastoma cell lines to describe the landscape of extrachromosomal circular DNA in neuroblastoma.
Project description:Circle-seq data for 21 primary neuroblastoma samples supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).
Project description:The majority of sunlight-associated melanomas carry a unique UV-related C to T mutation signature at dipyrimidine sites. UVB radiation is known to induce cyclobutane pyrimidine dimers (CPDs) as the major form of DNA damage, but the mechanism of how these DNA lesions lead to mutations is unknown. To map the genome-wide distribution of CPDs at single base resolution, we developed a new method, circle damage sequencing (circle-damage-seq). We found that in human cells CPDs form in a specific tetranucleotide sequence context (5’PyPy<>PyT/A), but this alone does not explain the mutation patterns. To test whether mutations arise at CPDs by cytosine deamination, we next applied a modification of circle-damage-seq and mapped UVB-induced cytosine-deaminated CPDs. We observed that the transcription start sites (TSS) are the sequences most protected from CPDs and deaminated CPDs. The strongest spike of CPDs and deaminated CPD lesions was found immediately upstream of the TSS, suggesting a mutation-promoting role of bound transcription factors. Most significantly, the genome-wide dinucleotide and trinucleotide sequence specificity of deaminated CPDs matched the prominent mutation signature found in melanomas. Our data identifies the cytosine-deaminated CPD as the leading premutagenic lesion responsible for the vast majority of mutations in sun-exposure-linked melanomas.
2020-10-22 | GSE159807 | GEO
Project description:Off-target analysis of CRISPR-Cas9 with CIRCLE-seq method
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset
Project description:This dataset comprises Circle-seq data for 12 neuroblastoma cell lines supporting Koche et al. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma (2020).