According to Google Scholar, the original SHAPE-Seq experiment paper in PNAS has over 100 citations! For those unfamiliar with it, SHAPE-Seq uses chemical probing and next generation sequencing to characterize RNA structures in very high throughput and with nucleotide resolution. It is built off of the powerful SHAPE chemistry developed by the Weeks lab at UNC Chapel Hill and the Illumina next generation sequencing platform. SHAPE-Seq and its descendants are changing the way we ask questions about the role of RNA structure across biology, and are starting to bring RNA structural biology into the omics era.
And we continue to improve and innovate on the SHAPE-Seq technology – see our recent NAR paper about optimizing SHAPE-Seq to provide highly reproducibly data, and our release of SHAPE-Seq v2.0 which can be performed in a more ‘universal’ kit-like fashion. And we are happy to say that all of our published SHAPE-Seq data is being deposited in the RNA Mapping Database (RMDB) for all to use!
We are always interested in helping others get started with SHAPE-Seq, and in seeing the community grow. To that end we have started a SHAPE-Seq mailing list where people can email experimental and computational questions on getting started with the experiment and in interpreting the data. Please email Julius (jblucks <at> cornell (dot) edu) to get signed up.
A big thank you to the community that helped SHAPE-Seq turn 100, and to the future community that helps it keep growing!