Volume 13 Issue 11, November 2018

This protocol update describes silica-based approaches for purification of DNA from ancient bone, tooth and sediment samples. The optimized buffers yield short DNA fragments compatible with high-throughput sequencing library preparation.

This protocol describes how to implement and apply an adaptive light-sheet microscopy framework (AutoPilot). The procedure can be used to introduce AutoPilot in an existing microscope or to set up a new adaptive multiview light-sheet microscope.

Spatial Transcriptomics combines histological staining and spatially resolved RNA-sequencing data from tissue sections. This protocol describes how to implement this method with mammalian tissue.

Hydroxyl-radical footprinting provides a wealth of data on the structure of nucleic acid–protein complexes. HYDROID is a software tool used to quantify footprinting data from gel electrophoresis images and integrate them with structural models.

This protocol describes how to produce cell-laden microfibers using capillary microfluidic devices. The devices enable spinning of increasingly complex microfibers, which can function as building blocks for 3D cell culture and tissue engineering.

Here, the authors describe how to use BasePlayer, an interactive and user-friendly software that facilitates the identification of causative mutations from next-generation sequencing data.

This protocol provides a procedure by which Drosophila ovarioles are dissected with or without the epithelial sheath and placed in a closed chamber that mimics physiological conditions for imaging.

This protocol describes CIRCLE-seq (circularization for in vitro reporting of cleavage effects by sequencing), a sensitive and unbiased method for defining the on-target and off-target activity of CRISPR–Cas9 nucleases genome-wide.

This protocol addresses the need to define informative priors to apply ensemble modeling in systems biology. The protocol collects parameters, assesses their plausibility and creates log-normal probability distributions for use as informative priors.

This protocol describes the synthesis of magnetic resonance tuning (MRET) sensors. The sensors consist of two magnetic components separated by a linker and can be modularly designed for targets such as enzymes, nucleic acid sequences, and pH values.

This protocol describes how to generate transgenic zebrafish expressing a barcode array that can be edited by CRISPR–Cas9 at multiple developmental stages. Single-cell RNA sequencing of edited barcodes and cellular transcriptomes allows reconstruction of lineage relationships.

This protocol describes the synthesis, characterization, and calibration of a nanoscale fiber-optic force sensor. The sensor can be used to detect sub-piconewton forces and acoustic waves in biological environments by means of optical readouts.