Volume 11 Issue 11, November 2016

Electron cryo-tomography produces 3D pictures of unique objects such as viruses, organelles or cells. This is a protocol for macromolecular structure determination from tomographic data using subtomogram averaging in the RELION software.

This protocol describes a simple pipeline for imaging FRET biosensor probes with two-photon laser scanning microscopy (TPLSM). Validated FRET standards are described that can be used with any TPLSM setup to ensure sensitive detection of FRET ratios.

G&T-seq enables sequencing of DNA and mRNA from the same single cell, allowing the effects of genomic variation on transcription to be studied. It is compatible with any WGA method and so can be tailored to specific applications.

Ramani et al. describe a protocol for in situ DNase Hi-C as an alternative to traditional Hi-C methods that use restriction enzymes. The use of DNase I for chromatin digestion circumvents the resolution limit imposed when relying on genomic restriction sites.

Small-angle X-ray and neutron scattering are used to extract structural parameters and derive structural models of macromolecules in solution. The preparation of pure, monodisperse samples and exactly matching solvent blanks is crucial to the experiments' success.

This protocol extends the use of genome editing technology to the modeling or correction of large chromosomal rearrangements and short nucleotide repeat expansions. The authors use the CRISPR/Cas system to edit human induced pluripotent stem cells.

This protocol describes how to remodel sheep and mouse fibroblast nuclei into spermatid-like structures by exogenous expression of the protamine 1 gene. Blastocyst formation following somatic cell nuclear transfer in sheep oocytes is also described.

This protocol uses restriction enzymes to produce isolength tags that are concatenated and sequenced to allow genome-wide genotyping and quantification of DNA methylation levels.

The protocol describes how to make transparent graphene neural electrodes for implantation onto the surface of the cerebral cortex in rodents and subsequent neural analysis by fluorescence microscopy, electrophysiology, optical coherence tomography, and optogenetics.

This protocol describes how to differentiate and image human embryonic stem cells on micropatterned colonies to create radially organized domains of the germ layers mimicking embryonic gastrulation in vitro.

This 96-well-plate ‘real-time quaking-induced conversion’ assay allows the detection of abnormal prion protein in human brain and CSF samples. It can be applied to study many protein misfolding diseases, as well as for drug screening and prion strain discrimination.

This protocol from Fu et al. describes the use of self-assembled DNA nanostructures as assembly scaffolds to spatially arrange multienzyme complexes and probe their interactions.

This protocol describes how to derive haploid human embryonic stem cells (ESCs) by parthenogenesis, and how to isolate and maintain them by cell sorting. Haploid human ESCs have a wide differentiation potential and are useful for genetic screening.

This protocol describes the design and synthesis of amphiphilic gold nanocrystals coated with polymer brushes and their self-assembly into plasmonic vesicles.