Visualizing DNA folding and RNA in embryos at single-cell resolution

• Main Authors: Mateo, Leslie J., Sedona E. Murphy, Hafner, Antonina, Cinquini, Isaac S., Walker, Carly A., Boettiger, Alistair N.
• Format: Dataset
• Language: English
• Published: Zenodo 2019
• Subjects: ORCA, super-resolution, 3D genome, spatial omics; Orca
• Online Access: https://dx.doi.org/10.5281/zenodo.4741213; https://zenodo.org/record/4741213

See: https://www.nature.com/articles/s41586-019-1035-4 for a description of the approach Dataset organization: The dnaData files contain 3D chromatin paths measured using Optical Reconstruction of Chromatin Architecture are recorded in nanometers, (x,y,z positions). Individual paths are also indexed by cell ID number, embryo ID number, embryo segment type ID number, brightness, and genomic position. The expression level of 29 RNA targets in the corresponding cells are indexed in the accompanying rnaData document. The cell ID number can be used to link the RNA expression and DNA structure from the same cells. RNA expression is provided in molecule counts per cell for cytoplasmic mRNA targets, and in arbitrary brightness units for intronic RNA targets.