Protocols

The authors present a protocol for genome-wide clustered regularly interspaced short palindromic repeat screening of three-dimensional neurospheres.

Detect-seq (dU-detection enabled by C-to-T transition during sequencing) enables off-target evaluation of programmable cytosine base editors. DNA is chemically labeled, and the editing intermediate dU is enriched for sequencing by biotin pull-down.

ProTracer is a genetic lineage–tracing technology that uses two recombinases to allow lifelong, noninvasive monitoring of cell proliferation for specific cell lineages in live animals.

A step-by-step guide providing biomedical researchers instructions for implementing spatial- and Fourier-domain ptychography to existing setups with minimal hardware modifications.

The authors describe the fabrication, assembly and long-term implantation of ultraflexible neural probes for the simultaneous recording of neural activity and neuromodulation in rodents.

A protocol for the generation of medulloblastoma and high-grade glioma organoids by electroporating, respectively, cerebellum and forebrain organoids, along with procedures for their use in drug screening, lineage tracing, co-culture and in vivo assays.

Cellulose is a burgeoning feedstock for more sustainable alternatives to fossil fuel-based materials. This protocol uses a cellulose-dissolving ionic liquid electrolyte with nuclear magnetic resonance methods to provide high-resolution structural analysis of cellulose.

The authors describe spiral volumetric optoacoustic tomography for the visualization of contrast agent perfusion and biodistribution in mice, featuring excellent scalability to achieve spatial resolution down to 90 µm or whole-body scans in <2 s.

We present the design, assembly and implementation of a molecular-electromechanical system composed of a tetrahedral DNA nanostructure immobilized on a graphene field-effect transistor for unamplified detection of trace amounts of analytes in biofluids.

We present a protocol for the encapsulation and stabilization of enzymes by using hydrogen-bonded organic frameworks (HOFs)—enzyme@HOF-101—along with procedures for their material characterization and testing of their biocatalytic performance.

This protocol enables the generation of human forebrain organoids from induced pluripotent stem cells with the intrinsic ability to assemble functionally integrated bilateral optic vesicles.

AbEMap generates large ensembles of docked antigen–antibody structures based on the structure of an antigen and either the structure or the sequence of an antibody. For each antigen residue, a likelihood score for being part of the epitope is obtained.

A protocol for the directed differentiation of human pluripotent stem cells into distal lung organoids that can be used to model interstitial lung disease, viral infection and human lung development, along with procedures for their analysis.

This CRISPR-Combo system enables efficient multiplexed orthogonal genome editing and transcriptional activation in plants. Here, the use of CRISPR-Combo is demonstrated for speed breeding of transgene-free, genome-edited Arabidopsis and enhancing rice regeneration with more germline mutations.

This protocol for Multiplexed Intermixed CRISPR Droplets uses microfluidics to create droplets containing Cas9, multiplexed single-guide RNAs and corresponding DNA barcodes, allowing large-scale genetic screens to be performed in F0 zebrafish.

This protocol describes the use of Retro-Cascorder to make temporally resolved transcriptional recordings in Escherichia coli DNA, using a retron reverse transcriptase to store transcriptional events in a unidirectionally expanding CRISPR array via acquisition by CRISPR–Cas integrases.

The authors present a surgical approach to isolate neural cells from macaques with fast and efficient steps, combined with optimized culturing conditions, to improve the yield and quality of cell populations for downstream analyses

The CIRI-long protocol combines circular reverse transcription and long-read nanopore sequencing to capture full-length circular RNA isoforms, allowing their functional characterization.

Graphene-based single-molecule junctions, integrated with an electrical circuit, facilitate the detection of electronic, optical and mechanical properties of reactions at the molecular scale.

Micro Capture-C is a chromatin conformation capture method for visualizing reproducible three-dimensional contacts of regulatory regions in the genome at base-pair resolution.