Extrachromosomal Circular DNA are composed of chromatin and replicate in the nucleus of the cell during cell division. Unlike typical chromosomes, they are composed of circular fragments of DNA, up to only a few million base pairs in size and contain no centromere or telomere. Extrachromosomal Circular DNA Extrachromosomal circular DNA (eccDNA) is circular DNA found in the nuclei of plant and animal cells, including human cells, in addition to chromosomal DNA. eccDNA can be from 200 up to 5 million base pairs in length. eccDNA has been found in the nuclei of human cancer cells and shown to carry many copies of
Single-cell DNA template strand sequencing Library construction proceeds as normal for Illumina paired-end sequencing. Multiplexing PCR primers are then ligated to the PCR amplicons with hexamer barcodes identifying which cell each fragment they are derived from. Unlike single cell sequencing protocols, Strand-seq does not utilize multiple displacement amplification or MALBAC for DNA amplification. Rather, it is solely dependent on PCR. The majority of current applications for Strand-seq start by aligning sequenced reads to a reference genome. Alignment can be performed using a variety of short-read aligners such as BWA and Bowtie. By aligning Strand-seq reads from a single cell to the reference genome, the inherited