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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.
This Protocol Extension describes how to prepare plant tissue to enable Spatial Transcriptomics profiling. Spatial Transcriptomics is achieved through the combination of histological staining of the plant tissue with spatially resolved RNA sequencing.
This protocol describes production and bioinformatics analysis pipelines for E/L Repli-seq, an extension of the earlier Repli-chip protocol, allowing rapid genome-wide replication-timing analysis by next-generation sequencing.
This protocol extension describes DNA-free genome editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. The authors' previously published protocol for genome editing of wheat used CRISPR/Cas9 plasmids.
Here the authors provide an extension to their earlier RNA interactome capture protocol. This Protocol Extension describes RBDmap—a method to identify the regions of RNA-binding proteins engaged in native interactions with RNA, in a proteome-wide manner.
Here the authors provide an extension of their original FLOTAC protocol, describing the Mini-FLOTAC technique, optimized to perform diagnosis of helminth and protozoan infections in humans and animals where centrifugation may not be practical.
Targeted DamID (TaDa) extends DamID to enable cell-type-specific profiling of genome-wide protein binding. Transcription factor binding sites, RNA Pol II occupancy and chromatin states can be studied to provide insights into cell-fate specification.