Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26223147_1.fastq.gz | Fastqsanger.gz | |||
| SRR26223147_2.fastq.gz | Fastqsanger.gz |
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Project description:Background Sporothrix brasiliensis and Sporothrix schenckii are the main etiological agents of sporotrichosis. These pathogens release extracellular vesicles (EVs), which are key transport structures involved in virulence and host–pathogen interactions. EVs from S. brasiliensis and S. schenckii have been exclusively under liquid culture conditions, with analyses focused on their protein composition and functional roles. However, noinformation is currently available regarding the small molecule composition of Sporothrix EVs, and the extent to wich S. schenckii and S. brasiliensis share or differ in their EVs cargo remain unknown. Methods We isolated EVs from S. brasiliensis (strain 5110) and S. schenckii (strain 1099-18) following cultivation on solid medium, and characterized the samples using a combination of nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), proteomics, and small molecule identification. Based on the EV composition, subsequent analyses included biochemical assay to assess cell-assocaited enzyme activity and a functional model of Sporothrix adhesion to type I collagen in the presence of isoleucine-proline-isoleucine (IPI), a peptide component found in EVs produced by both S. schenckii and S. brasiliensis. Results EVs from both S. brasiliensis and S. schenckii exhibited a high protein diversity, encompassing components related to essential cellular processes and virulence mechanisms. Only a small fraction of the identified proteins was shared between the two species, and a similar pattern was observed for the small molecules. Among the common molecules was IPI, previously described in Cryptococcus EVs. IPI is an inhibitor of dipeptidyl peptidase IV (DPP4), which was detected on the surface of S. brasiliensis and S. schenckii. Both IPI and an antibody against DPP4 effectively reduced Sporothrix adhesion to type I collagen, a major component of the host extracellular matrix. Conclusion Our study reveals an unprecedented level of proteomic and metabolomic complexity in Sporothrix EVs, uncovering novel molecular features and identifying IPI as an inhibitor of fungal adhesion to collagen.
2025-09-15 | PXD066550 | Pride
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: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
Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO