Project description:Our study is a large-scale evaluation of de novo peptide sequencing tools using both publicly and proprietary heterogeneous datasets spanning multiple species, mass spectrometers, post-translational modifications, and a wide range of use cases. This dataset contains a publicly available subset of this dataset.
The dataset includes raw MS/MS spectra in their original vendor formats as well as in mzML and Mascot Generic Format (MGF). Additionally, peptide spectral hits (PSMs) identified through a database search and rescoring workflow, along with the dataset-specific protein databases used for annotation, are provided.
Project description:Purpose: The goals of this study are to introduce a new genome editing tool, which has the higher editing scope than the original genome editing tools. Methods: First, we transfected PE2 (the original prime editing tool, prime editor2), PE3 (the original prime editing tool, prime editor3) and HOPE (the new tool we developed in this study) vectors into human cells, respectively. Then, we harvested the genomic DNA form the transfected cells and amplified the specified amplicons. Finally, we used targeted amplicon sequencing approach to compare the editing efficiency and presion of the new tool with the original reported tools. Results: Our new genome editing tool improves the editing efficiency of prime editing without increasing the risk of undesired indels formation. Conclusions: We deleveped a new genome editing tool to increase the likelihood of successful gene engineering.
Project description:There is a challenge of thyroid cancer versus benign follicular denoma differential diagnostics using fine-needle biopsy. RNA expression profiles can be used to identify biomarkers suitable for molecular diagnostics. Here we present raw RNA sequencing data obtained during Oncobox platform observational study for 96 human pathological thyroid biosamples. Data are compatible with Oncobox Atlas of Normal Tissue Expression (ANTE) database including profiles for healthy thyroid tissues. . The data provided are helpful to those implicated in thyroid cancer research and diagnostics, and in comparative analyses of human cancers.
Project description:In this study, 7530 newborn pancreatic β-cells were analyzed by single-cell sequencing. Cell Ranger was used to compare the original sequencing data, count the genome, filter background cells and cell transcript UMI, and use cell barcode to generate gene-barcode matrix. Then the samples were grouped, gene expression analysis, etc., and the statistical results of each sample sequencing data were output
Project description:DDA analysis of samples of commercial tryptic peptides of BSA which had been either untreated ("original"), conjugated with the Harnimarta et al sequencing reagent ("conj") or conjugated and exposed to alkaline cleavage conditions ("seq"). Data was searched in Proteome Discoverer 2.5 using a 58.017 Da for the sequencing reagent dynamic modification. The associated BSA2 fasta includes a synthetic sequence to generate in silico tryptic peptides representing the original BSA tryptic peptides lacking a single N-terminal amino acid.
