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In this Protocol Extension, the authors extend their original Protocol used to generate a genome-scale metabolic model for a single strain to enable multi-strain models to be made, which can be used to study pan-metabolic capabilities and strain-specific differences across a species.
Circulating cell-free DNA (cfDNA) is shed in the bloodstream by normal and tumor cells and is a valuable liquid biopsy tool. This protocol describes a low-input approach to enrich methylated DNA fragments from cfDNA and prepare sequencing libraries.
Selective ribosome profiling (SeRP) reveals nascent chain length–resolved binding profiles of a co-translationally acting factor and relies on selective enrichment of factor-engaged monosomes. This protocol describes how to perform the procedure in yeast.
This Protocol Extension describes procedures used to identify cell-type-specific transcriptomes in mice without sorting cells. The approach combines cell-specific RNA labeling and chemical modifications to introduce T>C conversions in the labeled RNA.
This protocol describes the analysis of stable isotope (13C and 15N) incorporation into polar metabolites in central carbon metabolic pathways using HILIC separation and selected reaction monitoring with a hybrid triple quadrupole mass spectrometer.