Nature Protocols Contents: Volume 13 Number 11

TABLE OF CONTENTS November 2018 Volume 13, Issue 11 Protocol Extensions Protocol Updates Protocols Advertisement   Do you have a career question? The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud.  Listen today! Advertisement New Poster on: Epitranscriptome regulation Download a new poster from Nature Structural & Molecular Biology on epitranscriptome regulation, a key mechanism affecting gene expression as well as cellular functions, development and disease. Available free online Produced with support from  Accent Therapeutics, Inc.    Protocol Extensions Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays    pp2425 - 2446 Stefania Giacomello & Joakim Lundeberg doi:10.1038/s41596-018-0046-1 This Protocol Extension describes how to prepare plant tissue to enable Spatial Transcriptomics profiling. Spatial Transcriptomics is achieved through the combination of histological staining of the plant tissue with spatially resolved RNA sequencing. Protocol Updates Extraction of highly degraded DNA from ancient bones, teeth and sediments for high-throughput sequencing    pp2447 - 2461 Nadin Rohland, Isabelle Glocke, Ayinuer Aximu-Petri & Matthias Meyer doi:10.1038/s41596-018-0050-5 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. Protocols A practical guide to adaptive light-sheet microscopy    pp2462 - 2500 Loïc A. Royer, William C. Lemon, Raghav K. Chhetri & Philipp J. Keller doi:10.1038/s41596-018-0043-4 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. Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections    pp2501 - 2534 Fredrik Salmén, Patrik L. Ståhl, Annelie Mollbrink, José Fernández Navarro, Sanja Vickovic et al. doi:10.1038/s41596-018-0045-2 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. Structural interpretation of DNA–protein hydroxyl-radical footprinting experiments with high resolution using HYDROID    pp2535 - 2556 Alexey K. Shaytan, Hua Xiao, Grigoriy A. Armeev, Daria A. Gaykalova, Galina A. Komarova et al. doi:10.1038/s41596-018-0048-z 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. Design of capillary microfluidics for spinning cell-laden microfibers    pp2557 - 2579 Yunru Yu, Luoran Shang, Jiahui Guo, Jie Wang & Yuanjin Zhao doi:10.1038/s41596-018-0051-4 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. Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer    pp2580 - 2600 Riku Katainen, Iikki Donner, Tatiana Cajuso, Eevi Kaasinen, Kimmo Palin et al. doi:10.1038/s41596-018-0052-3 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. Live imaging of stem cells in the germarium of the Drosophila ovary using a reusable gas-permeable imaging chamber    pp2601 - 2614 Amy Reilein, Elisa Cimetta, Nina M. Tandon, Daniel Kalderon & Gordana Vunjak-Novakovic doi:10.1038/s41596-018-0054-1 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. Defining CRISPR–Cas9 genome-wide nuclease activities with CIRCLE-seq    pp2615 - 2642 Cicera R. Lazzarotto, Nhu T. Nguyen, Xing Tang, Jose Malagon-Lopez, Jimmy A. Guo et al. doi:10.1038/s41596-018-0055-0 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. Defining informative priors for ensemble modeling in systems biology    pp2643 - 2663 Areti Tsigkinopoulou, Aliah Hawari, Megan Uttley & Rainer Breitling doi:10.1038/s41596-018-0056-z 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. A magnetic resonance tuning sensor for the MRI detection of biological targets    pp2664 - 2684 Tae-Hyun Shin, Sunghwi Kang, Sohyeon Park, Jin-sil Choi, Pan Ki Kim et al. doi:10.1038/s41596-018-0057-y 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. Large-scale reconstruction of cell lineages using single-cell readout of transcriptomes and CRISPR–Cas9 barcodes by scGESTALT    pp2685 - 2713 Bushra Raj, James A. Gagnon & Alexander F. Schier doi:10.1038/s41596-018-0058-x 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. Nanoscale fiber-optic force sensors for mechanical probing at the molecular and cellular level    pp2714 - 2739 Yuesong Shi, Beril Polat, Qian Huang & Donald J. Sirbuly doi:10.1038/s41596-018-0059-9 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. Advertisement Nature Briefing is an essential round-up of science news, opinion and analysis, free in your inbox every weekday. With Nature Briefing, we'll keep you updated on the latest research, so you can focus on yours. Click here to sign up.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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