Profiling of Alu cDNA in the cytoplasmic fraction of human RPE cells

We performed next-generation sequencing of cytoplasmic fractions of primary human RPE cells. Cytoplasmic sample were size-fractionated on a Blue Pippin device (Sage Science) for size restriction to 200–800-nt long species to eliminate genomic DNA contamination and embedded Alu elements. We found that Alu S predominated (61% of Alu reads), with lower levels of Alu J (31%) and Alu Y (8%). No significant difference in the overall distribution of these Alu sequences that mapped to RPE-specific 47 and non-RPE-specific genes was observed. However, we did identify a cluster of Alu sequences within 2,000 bp of 7 single-nucleotide variant loci statistically associated with AMD48. Examination of cytoplasmic DNA in human RPE cells