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  1. No Access

    Article

    Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

    Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for map** transposa...

    Ansuman T. Satpathy, Jeffrey M. Granja, Kathryn E. Yost, Yanyan Qi… in Nature Biotechnology (2019)

  2. No Access

    Article

    HiChIRP reveals RNA-associated chromosome conformation

    Modular domains of long non-coding RNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here, we present HiChIRP, a method leveraging bio-orthogonal chemistry and o...

    Maxwell R. Mumbach, Jeffrey M. Granja, Ryan A. Flynn, Caitlin M. Roake… in Nature Methods (2019)

  3. No Access

    Article

    An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

    The Omni-ATAC protocol improves the signal-to-background ratio in chromatin accessibility profiles and is suitable for a range of cell lines and primary cell types, as well as frozen tissue.

    M Ryan Corces, Alexandro E Trevino, Emily G Hamilton, Peyton G Greenside… in Nature Methods (2017)

  4. No Access

    Article

    HiChIP: efficient and sensitive analysis of protein-directed genome architecture

    HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.

    Maxwell R Mumbach, Adam J Rubin, Ryan A Flynn, Chao Dai, Paul A Khavari… in Nature Methods (2016)

  5. No Access

    Article

    Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE

    icSHAPE allows transcriptome-wide RNA structure profiling in living cells. It uses a clickable SHAPE reagent to enable biotin-based enrichment of SHAPE-modified RNA, reducing the necessary sequencing depth.

    Ryan A Flynn, Qiangfeng Cliff Zhang, Robert C Spitale, Byron Lee… in Nature Protocols (2016)