Nuclear DNA the bases are held together by hydrogen bonds. Nuclear DNA and mitochondrial DNA differ in many ways, starting with location and structure. Nuclear DNA is located within the nucleus of eukaryote cells and usually has two copies per cell while mitochondrial DNA is located in the mitochondria and contains 100-1,000 copies per cell. The structure of nuclear DNA chromosomes is linear with open ends and includes 46 chromosomes containing 3 billion nucleotides. Mitochondrial DNA chromosomes usually have closed, circular structures, and contain for example 16,569 nucleotides in human. Nuclear DNA is diploid, ordinarily inheriting the DNA from two parents, while
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