Similar Datasets
Project description:Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023). However, these experiments were carried out in our lab-based experimental medium, tryptone and yeast extract (TY-). To understand whether culturing these species within a medium that more closely mimics their natural environment alters the interaction, we evaluated both monoculture and coculture growth between the dental caries pathogen Streptococcus mutans and oral commensal species Streptococcus oralis in a half TY- / half human saliva mix that was optimally chosen based on our initial characterization of oral streptococci behaviors in medium mixes containing saliva. Our results surprising show that inclusion of saliva enhances the competition of Streptococcus mutans against commensal streptococci through upregulation of carbohydrate uptake and glycolytic pathways.
2023-08-22 | GSE239483 | GEO
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
2021-11-17 | E-MTAB-10548 | biostudies-arrayexpress
Project description:Solid tumors were histopathologically categorized into carcinomas and sarcomas and analyzed based on structural variations specific to each group. To investigate this, we utilized whole genome sequencing (WGS) data from dogs with solid tumors, including carcinomas and sarcomas. Structural variations, which induce extensive base changes, significantly impact tumor development. Through our analysis, we identified 146,847 structural variations within the solid tumor data. By comparing each solid tumor group, we identified both common genes affecting tumors across groups and differential genes unique to carcinomas and sarcomas. This finding suggests that understanding the specific genetic alterations associated with each tumor type can enhance the accuracy of diagnosis, inform treatment strategies, and improve prognostic assessments.
2025-12-01 | E-MTAB-14410 | biostudies-arrayexpress
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:This dataset holds three runs of our new Atrandi-SPC based single-cell WGS protocol, one for each lysis protocol (R1-R3 in the study)
2026-05-30 | E-MTAB-15286 | biostudies-arrayexpress