Rxivist logo

Rxivist combines preprints from bioRxiv with data from Twitter to help you find the papers being discussed in your field. Currently indexing 73,613 bioRxiv papers from 320,330 authors.

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9

By Lindsey Montefiori, Liana Hernandez, Zijie Zhang, Yoav Gilad, Carole Ober, Gregory Crawford, Marcelo Nobrega, Noboru Jo Sakabe

Posted 22 Nov 2016
bioRxiv DOI: 10.1101/087890 (published DOI: 10.1038/s41598-017-02547-w)

ATAC-seq is a high-throughput sequencing technique that aims at identifying DNA sequences located in open chromatin. Depending on the cell type, ATAC-seq may yield a high number of mitochondrial sequencing reads (~20-80% of the reads). As the regions of open chromatin of interest are usually located in the nuclear genome, mitochondrial reads are typically discarded from the analysis. To decrease wasted sequencing, we performed targeted cleavage of mitochondrial DNA using CRISPR/Cas9 and 100 mtDNA-specific guide RNAs. We also tested a modified ATAC-seq protocol that does not include detergent in the cell lysis buffer. Both treatments resulted in considerable reduction of mitochondrial reads (1.7 and 3-fold, respectively). The removal of detergent, however, resulted in increased background and fewer peaks identified. The highest number of peaks and highest quality data was obtained by preparing samples with the original ATAC-seq protocol (using detergent) and treating them with anti-mitochondrial guide RNAs and Cas9. This strategy could lead to considerable cost reduction and improved peak calling when performing ATAC-seq on a moderate to large number of samples and in cell types that contain a large amount of mitochondria.

Download data

  • Downloaded 1,653 times
  • Download rankings, all-time:
    • Site-wide: 3,767 out of 73,690
    • In genomics: 687 out of 4,889
  • Year to date:
    • Site-wide: 43,950 out of 73,690
  • Since beginning of last month:
    • Site-wide: 43,950 out of 73,690

Altmetric data


Downloads over time

Distribution of downloads per paper, site-wide


PanLingua

Sign up for the Rxivist weekly newsletter! (Click here for more details.)


News