Project description:We investigated the effects of different sample preparation factors on RNA-seq experiments, including RNA concentration, library storage time, and cryopreserved condition, by comparing their sequencing biases, gene expression profiles, and biological function using primary B cell and CD4+ cell blood samples in healthy subjects.
Project description:DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we developed a sample preparation method to measure RT genome-wide that does not require fixation.
Project description:A collection of digital automated proteomic sample preparation protocols detail three optimized step-by-step methods to: (A) lyse Gram-negative bacteria and fungal cells; (B) quantify the amount of protein extracted; and (C) normalize the amount of protein and set up tryptic digestion. These protocols have been developed to facilitate rapid, low variance sample preparation of hundreds of samples, be easily implemented on widely-available Beckman-Coulter Biomek automated liquid handlers, and allow flexibility for future protocol development
Project description:Major advances have been made to improve the sensitivity of mass analyzers, spectral quality, and the speed of data processing enabling more comprehensive proteome discovery and quantitation. While focus has recently begun shifting toward robust proteomic sample preparation efforts, a high throughput proteomics sample preparation is still lacking. We report the development of a highly-automated universal 384-well plate sample preparation platform with high reproducibility and adaptability for extraction of proteins from cells within a culture plate. Digestion efficiency was excellent in comparison to a commercial digest peptide standard with minimal sample loss while improving sample preparation throughput by 20- to 40-fold (<1 min/sample for entire process from cells to clean peptides). Analysis of six human cell types, which included two primary cell samples, identified and quantified approximately 4,000 proteins for each sample in a single HPLC-MS/MS injection with only 100 -10,000 cells, thus demonstrating universality of the platform.
Project description:In this work, we propose a new high-throughput ultrafast method for large scale proteomics approaches by speeding the classic filter aided sample preparation protocol, FASP. The new US-FASP method matches the analytical minimalism roles as time, cost, sample requirement, reagent consumption, energy requirements and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all the advantages of the filter aided sample preparation protocol are maintained.