Volume 16 Issue 12, December 2021

This protocol provides a step-by-step workflow for ATAC-Me, an integrated method for simultaneously probing DNA methylation and chromatin accessibility from a single DNA fragment library.

Biological systems can now be studied at the single-cell level using mass spectrometry. In Single Cell ProtEomics (SCoPE2), a carrier sample is used to enhance peptide sequence identification with multiplexed analysis using isobaric mass tags.

Raman spectroscopy is increasingly being used in biological assays and studies. This protocol provides guidance for performing chemometric analysis to detect and extract information relating to the chemical differences between biological samples.

Yang and colleagues describe a rolling circle amplification-based approach for synthesizing multifunctional physically and dynamically cross-linked DNA hydrogels for efficient cell isolation and delivery.

Park and colleagues describe the synthesis of methacrylated photocurable silk fibroin bioink for digital light processing 3D bioprinting as well as fabrication of biocompatible organ-mimicking hydrogel structures for trachea tissue engineering.

MALDI-TOF mass spectrometry (MS) can detect multiple compounds simultaneously. This protocol describes how to develop and optimize high-throughput, cell-based assays that use MALDI-TOF MS to detect drug uptake or biochemical markers of drug activity.

Gouverneur et al. present a protocol for multigram synthesis of two chiral urea-based hydrogen-bonding phase-transfer catalysts for asymmetric nucleophilic fluorinations of target compounds, including detailed synthesis and purification procedures.

GUIDE-seq (genome-wide unbiased identification of double-stranded breaks enabled by sequencing) is a sensitive, unbiased, genome-wide method for defining the specificity of genome-editing nucleases in living cells.

This two-phase task assesses the extent to which animals can discriminate and remember object locations. Unlike in similar tasks, the load on pattern separation during memory encoding—when pattern separation is thought to occur—varies.

The trRosetta server, a web-based platform for fast and accurate protein structure prediction, is powered by deep learning and Rosetta. This protocol includes procedures for using the web-based server as well as the standalone package.

Human pluripotent stem cell aggregates are formed, embedded in Matrigel and directed to differentiate to heart-forming organoids by the chemical WNT pathway modulators CHIR99021 and IWP2.

This protocol describes experimental and computational procedures for genome-wide mapping of transcription factor binding at single-molecule resolution using methyl-transferase footprinting.

Sen and colleagues describe a protocol for the fabrication of silicon hollow-needle arrays to achieve tissue nanotransfection of mouse skin.