Volume 16 Issue 9, September 2021

This protocol describes a complete workflow for detecting significant contacts in Capture Hi-C data, including preprocessing, interaction calling and downstream analyses, based on the CHiCAGO pipeline and companion tools.

This protocol describes novoSpaRc, a computational pipeline for de novo reconstruction of spatial gene expression from single-cell RNA sequencing with the potential to incorporate spatial atlas data to improve the reconstruction.

This protocol enables explicit regional and functional division of functional elements of solid-state nanochannels to improve the sensitivity and specificity of bioanalysis in complex matrices.

This protocol describes how to use free-space angular-chirp-enhanced delay (FACED), an all-optical, passive and reconfigurable laser-scanning approach, to increase the imaging speed of various microscopy modalities.

The authors provide a protocol for fluorescence multiplex host cell reactivation, which uses reporter plasmids containing site-specific DNA lesions to assess DNA repair capacity in at least six major DNA repair pathways in live cells.

Metabolomics studies using large-scale NMR or mass spectrometry experiments on biofluids or tissues generate complex data. This protocol provides guidelines and software (supplied in Jupyter notebooks) for the statistical analysis of these data.

This high-throughput protocol for direct ex vivo real-time metabolic fingerprinting of biofluids uses a laser system and an automated sampling platform. It includes REIMS procedures for analyzing blood, urine, stool, saliva, sputum and breast milk.

This protocol describes isolation and long-read sequencing (using either the Oxford Nanopore or PacBio platforms) of nascent chromatin-associated RNAs from Arabidopsis seedlings and bioinformatic pipelines for profiling splicing and polyadenylation.

This protocol describes a high-throughput sequencing approach to identifying regulators of bacterial gene expression based on transposon insertion mutagenesis in a strain harboring a fluorescent reporter.

Radiotracers used in human positron emission tomography studies need to be prepared according to current good manufacturing practice. Here we use the synthesis of [¹¹C]ER176 as an example to show the translation of an experimental radiosynthesis to a current good manufacturing practice process.

The authors describe procedures for genome-wide quantification of histone modifications and chromatin-associated proteins after replication (chromatin occupancy after replication-seq) and for profiling their relative occupancy in nascent sister chromatids (sister chromatids after replication-seq).

This protocol describes how to rapidly isolate a specific cell type from mouse blood or tissues for mass-spectrometry-based metabolomics. Mice are infused with isotopically labeled compounds, and cells are isolated using antibody-coated magnetic beads.

Human pluripotent stem cells acquire cancer-related mutations during culture, which can impact their use in the clinic or in basic research. This protocol describes a computational pipeline to detect such mutations using RNA sequencing data.