Here is a sampling of some of the papers that guide our lab’s research. You can also find me on google scholar and pubmed. #: co-senior author; *: equal contribution.

High Sensitivity Profiling of Chromatin Structure by MNase-SSP

Here, we presented MNase-seq by single-strand profiling (MNase-SSP), a generalizable library preparation protocol to sensitively profile the fragments resulting from nucleolytic digestion of chromatin. We demonstrate that MNase-SSP captures different classes of minimally protected CTCF/Ctcf fragments possibly indicative of differential finger usage, and reveals subnucleosomal structure at murine embryonic stem cell promoters.

Ramani V#, Qiu R, Shendure J#

Cell Reports

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

Here we presented single-cell combinatorial indexing for measuring chromatin accessibility & RNA expression (sci-CAR), a high-throughput single-cell sequencing method for simultaneously profiling chromatin accessibility and mRNA expression in thousands of single cells in a single experiment. We applied sci-CAR to A549 cells drugged with the glucocorticoid receptor agonist dexamethasone, as well as primary murine kidneys.

Cao J, Cusanovich DA*, Ramani V*, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C#, Shendure J#