Project description:S. aureus isolates from chronic rhinosinusitis patients and healthy individuals were cultured overnight. The strains belonged to clonal complexes CC7 (CSS66 and MIN142) and CC15 (CSS126 and MIN93) that are both prevalent in Germany. These isolates have previously been characterized in Tuchscherr, L., et al., Reduced Glycolysis and Cytotoxicity in Staphylococcus aureus Isolates from Chronic Rhinosinusitis as Strategies for Host Adaptation. Int J Mol Sci, 2024. 25(4). Cultures were diluted in TSB broth to an optical density (OD600) of 0.05 the following day, and samples were collected at 3- and 6-hours post-dilution. Total RNA was extracted at these time-points and subjected to RNA sequencing (RNA-seq).
Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.
Project description:LORAX-seq (Yang et al, DOI:https://doi.org/10.1016/j.molcel.2024.01.019) was used to identify the backtracked RNA in DIS3-depleted HCT116 DIS3-AID cells. Briefly, LORAX-seq was performed according to Yang et al. (2024) with following modifications. The Pol II complexes were immunoprecipitated with α‐Rpb1 CTD (ab5408, Abcam), followed by capture using a mixture of Dynabeads Protein-A and G. The magnetic beads were treated with recombinant Human TCEA1 protein (ab204205, Abcam) as per Yang et al. (2024), followed by isolation of eluted RNA using TRIZOL (Invitrogen). RNA was prepared for sequencing using the NEBNext Low-bias Small RNA library prep kit (NEB). The eluted RNA was mixed with QIAseq miRNA Library QC Spike-in (331535, Qiagen) as per manufacturer’s instructions. Sequencing libraries were visualized using an Agilent 2100 Tapestation and sequencing was done using the NextSeq 1000/2000 P2 cartridge (Illumina). We identified longer backtracked RNAs in DIS3-depleted cells than in control cells.