Project description:Cell-free DNA is generally in fragments around 200 bp. Genomic DNA from HCT116 cell is sonicated to around 200 bp to mimic cell-free DNA. This is a control assay to test the sensitivity of Infinium methylationEPIC array for low amount of fragmentized DNA.
Project description:To know the optimal amount of input library for HiSeq X Ten, the amount of input library was varied. Six lanes of sequencing on HiSeq X Ten was performed.
Project description:Critical protein therapeutics, such as antibodies and nanobodies, are often not encoded in reference genomes, limiting their accurate characterization via standard proteomics. Current methods rely on indirect inference, fragmented outputs, and labor-intensive workflows, which hinder functional insights and routine application. Here, we present a generalizable, end-to-end workflow for direct protein sequencing, combining streamlined sample preparation, AI-driven de novo peptide sequencing, and tailored assembly to reconstruct contiguous protein sequences. A novel composite scoring framework prioritizes longer assemblies and coverage, enhancing accuracy and reducing ambiguity. Validation across diverse protein modalities demonstrates its utility and ability to robustly reconstruct functionally critical regions essential for optimizing therapeutic efficacy, stability, and immunogenicity. This workflow advances precision proteomics with promising applications in therapeutic discovery, immune profiling, and protein engineering.
Project description:The goal of this study was to titrate the amount of adapters for picogram amounts of ChIP DNA to determine the optimal conditions for library generation. H3K4me3 ChIP DNA from human Raji cells was diluted to the indicated amount and sequencing libraries generated using a range of adapter concentrations. The optimal adapter:DNA ratios were sequenced in technical duplicate to determine the reproducibility at each starting ChIP DNA amount. Additionally, for two samples we altered the number of cycles during the PCR amplification to determine the effect of PCR on library complexity and read duplicates.
Project description:Here, we report an enrichment-based ultra-low input cfDNA methylation profiling method using methyl-CpG binding proteins capture, termed cfMBD-seq. We optimized the conditions of cfMBD capture by adjusting the amount of MethylCap protein along with using methylated filler DNA. Our data showed that cfMBD-seq performs equally to the standard MBD-seq (>1000 ng input) even when using 1 ng DNA as the input. cfMBD-seq demonstrated equivalent sequencing data quality as well as similar methylation profile when compared to cfMeDIP-seq. We showed that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of CpG islands. This new bisulfite-free ultra-low input methylation profiling technology has a great potential in non-invasive and cost-effective cancer detection and classification.