iscDNase-seq

The iscDNase-seq software tool represents an advancement in single-cell epigenomics, building upon the foundational single-cell DNase sequencing (scDNase-seq) assay to enhance the profiling of chromatin accessibility. It introduces a novel indexing strategy that utilizes terminal DNA transferase (TdT) and T4 DNA ligase for embedding unique cell barcodes into the ends of DNase-digested chromatin. This innovation allows for the detailed resolution of single-cell DNase hypersensitivity profiles from bulk-cell analyses. Through a sophisticated three-layer indexing approach, iscDNase-seq enables the genome-wide profiling of DNase hypersensitive sites (DHSs) across more than 15,000 single cells in a singular experimental run.

Topic

Epigenomics;Sequencing;Transcription factors and regulatory sites;Chromosome conformation capture;Gene transcripts

Detail

  • Operation: Demultiplexing;Peak calling;Expression correlation analysis

  • Software interface: Command-line interface

  • Language: MATLAB

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The Division of Intramural Research of NHLBI, NIH and the 4DN Transformative Collaborative Project Award, National Key Research and Development Project.

  • Input: -

  • Output: -

  • Contact: Bing Ni nibingxi@126.com ,Keji Zhao zhaok@nhlbi.nih.gov

  • Collection: -

  • Maturity: -

Publications

  • Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells.
  • Gao W, et al. Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells. Multiplex indexing approach for the detection of DNase I hypersensitive sites in single cells. 2021; 49:e56. doi: 10.1093/nar/gkab102
  • https://doi.org/10.1093/NAR/GKAB102
  • PMID: 33693880
  • PMC: PMC8191781

Download and documentation

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