Welcome to CutBase
The conventional chromatin immunoprecipitation sequencing (ChIP-seq) has been the gold standard technique to analyzing DNA-protein interactions. While ChIP-seq has the limitation of high amount of starting material, epitope masking, insolubility of protein complexes and high background noise. To overcome the limitations of ChIP assay, alternative strategies such as cleavage under targets and release using nuclease (CUT&RUN) and cleavage under target and tagmentation (CUT&Tag), were recently developed for mapping protein-DNA interactions from low input material with significantly improved resolution. Increasing high-resolution sequencing data are being generated, making the collection and annotation of these data being a big challenge for researchers to reuse.
Herein, we have developed the intergrated p latform, CutBase, to gather all these data and analyse the biological function of DNA bindings or histone modifications detected by CUT&RUN and CUT&Tag. Currently, CutBase has covered 135 cell types related to human diseases as well as normal cells from more than 200 published studies, including 3520 experiments of CUT&RUN and CUT&Tag from 19 species. All the data have been carefully processed with a streamlined analysis and evaluated with comprehensive quality control metrics using CUT&RUNtools 2.0. Moreover, peaks annotations and motif enrichments were analyzed using ChIPseeker and HOMER, respectively. Furthermore, we have also created a user-friendly web server for data query, exploration and visualization. CutBase extracts useful cis-regulatory information from these datasets and provides features that allow the biomedical research community to readily find and re-use these datasets. Therefore, CutBase is an integrated resource and analysis platform designed for comprehensive annotation and comparative analysis of chromatin profiling of cleavage under targets with CUT&RUN and CUT&Tag. The resulting CutBase is expected to be a valuable resource for transcriptional and epigenetic regulation studies. We are dedicated to maintaining CutBase and keeping the resource updated in the future.
CutBase: an integrated platform for chromatin profiling of cleavage under targetsPlease cite us with this Reference