Volume 14 Issue 3, March 2019

Here the authors provide an update to their 2013 protocol for using the PANTHER classification system, detailing how to analyze genome-wide experimental data with the newest version of PANTHER (v.14.0), with improvements in the areas of data quality, data coverage, statistical algorithms and user experience.

This protocol describes how to use a microfluidics system to produce human induced pluripotent stem cells at high efficiency and low cost using a small starting cell number.

A small laparotomy is carried out, and human cancer cells are implanted into the mouse bladder lumen. This reproduces the pathobiological events of human bladder cancer invasion in mice.

MAGeCKFlute is an algorithm for the analysis and visualization of CRISPR screen data. Starting from sequencing reads and an sgRNA library, the algorithm normalizes results and represents them as pathway enrichment classifications.

High-silica zeolites are widely used catalysts; those with different structural topologies are used for different applications. This protocol describes the assembly–disassembly–organization–reassembly (ADOR) process for preparing new zeolites.

This protocol describes a platform that integrates mammalian lncRNAs and whole genomes with the LongTarget program for genome-wide lncRNA-binding prediction. A choice of four pipelines allows searches to be tailored to different biological questions.

In this protocol, two mice meet in a tube and the more dominant one pushes out the other one. The social hierarchy of a group of mice can thus be measured.

This protocol describes an approach for super-resolution imaging by 10× physical expansion of the samples (X10 microscopy). In addition, the authors provide guidelines for determining the expansion and distortion factors.

This protocol describes how to make two-photon excitable genetically modified glutamate receptors for in vivo optogenetics.

This protocol describes the proximity ligation assay for RNA (PLAYR). PLAYR can be used to simultaneously detect at least 27 RNA transcripts using flow or mass cytometry and can be combined with protein detection via conventional antibody staining.

This protocol describes procedures for isolating and purifying uncondensed formaldehyde- and propionaldehyde-stabilized lignins from lignocellulosic biomass, and for recovering highly digestible cellulose and stabilized xylose.

Here, the authors provide protocols for CRISPR–Cas9-based genetic manipulation of Candida albicans, using a gene-drive strategy that allows genetic interaction networks to be established for this important fungal pathogen.

Here the authors describe CAPTURE, a versatile and sensitive protocol to detect spacer-acquisition events in native CRISPR arrays using nested PCR amplification and amplicon size selection.