(1/6) Excited to share that our OligoFISSEQ paper is up (nature.com/articles/s4159…)! We set out to develop single cell in situ #3Dgenome mapping methods. A fun collaborative effort led by @huy_sauce @ShyamtanuC and David Castillo, from @TingWu_Lab and @mamartirenom groups. 
(2/6) An idea that began with @SonCNguyen and Evan Daugharthy. The rest of the team including: @GuyNir5 @AntoniosLioutas @ElliotHershberg @Nuno_MCMartins @PaulReginato Mohammed Hannan @oligopain and @geochurch . Shout out to everyone @naturemethods for the great experience!
(3/6) To target and visualize genomic regions at genome-wide scale, we barcoded Oligopaints, increasing target capacity exponentially. We then visualize and map the targets by #InSituSequencing the barcodes using hybridization, synthesis, and ligation-based approaches.
(4/6) In human cells with 4-5 ligation rounds, we mapped 36 regions along 6 chromosomes, imaged regions across all 46 chromosomes, traced 46 regions along ChrX, combined with IF for DNA-protein imaging, combined with OligoSTORM to accelerate genome #SuperResolution, and more!
(5/6) OligoFISSEQ confirmed previous observations of preferential chromosome radial positioning as well as some new observations: 1. Chr 2, 3, 16, and 19 fold their p and q arms in significantly different ways. 2. Two Chr X conformations (loose and compact) in XY fibroblasts.
(6/6) We hope OligoFISSEQ will be of use to the #4DNucleome community. To better understand the impact of genome organization on biological function, it is necessary to map organization at local and global scales, at single cell and population levels. Please reach out with any ?s
