Project description:The amoebozoan Acanthamoeba castellanii is an important cause of infectious blindness and a key evolutionary outgroup to humans and fungi. We conducted complementary proteomic and transcriptomic profiling of an Acanthamoeba encystation timecourse. For the transcriptomics, we used both short read RNA-seq (Illumina) and long-read MAS-ISO-seq (PacBio). The bulk RNA-seq transcriptomics are reported here.
Project description:The amoebozoan Acanthamoeba castellanii is an important cause of infectious blindness and a key evolutionary outgroup to humans and fungi. We conducted complementary proteomic and transcriptomic profiling of an Acanthamoeba encystation timecourse. For the transcriptomics, we used both short read RNA-seq (Illumina) and long-read MAS-ISO-seq (PacBio). The long-read MAS-ISO-seq data are reported here.
Project description:Platinum-based drugs (Pt drugs) are widely used in cancer chemotherapy, yet their genome-wide DNA binding patterns remain incompletely understood. Here, we present Pt-seq, an antibody-assisted, genome-wide method for mapping Pt-DNA adducts at single-base resolution. By employing exo- and endo- nucleases to remove background DNA, Pt-seq enables highly robust and sensitive profiling of binding sites for cisplatin, oxaliplatin, lobaplatin, and a Pt(IV) complex. Using Pt-seq, we identified hundreds to a few thousand binding clusters that are 10-20 kb in length and highly consistent among different Pt drugs. Notably, these binding clusters predominantly localize to centromeric and rDNA regions. In cisplatin-resistant cells, we found significantly reduced binding within these regions, suggesting a potential role in drug resistance. Moreover, we found that de novo mutations in cancer cells can create novel binding sites for Pt drugs. Based on this, we demonstrated that ICR-191, an acridine orange compound capable of inducing G insertions, enhances cisplatin-DNA crosslinking and sensitizes cells to Pt drugs. Collectively, Pt-seq sensitively profiles Pt drug-DNA interactions and deepens our understanding of the genome-wide effect of chemotherapeutic drugs.
Project description:A culture of Acanthamoeba castellanii cells was infected with mimivirus. At specified times after infection, infected cells aliquots were subjected to total RNA extraction. Cy3 labeled cDNA was hybridized on custom designed Agilent oligonucleotide tiling microarrays covering both strands of the mimivirus genome.