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Cold Spring Harbor Laboratory

7 ARTICLES PUBLISHED IN JoVE

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Biology

In Situ Hybridization for the Precise Localization of Transcripts in Plants
Marie Javelle 1, Cristina F. Marco 1, Marja Timmermans 1
1Cold Spring Harbor Laboratory

The in situ hybridization protocol described here allows a direct localization of mRNA and small RNA expression at the cellular level with high sensitivity and specificity. The procedure is optimized for paraffin-embedded plant tissue sections, is applicable to a wide range of plants and tissues, and can be completed within ten days.

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Biology

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types
Haipeng Xing 1, Willey Liao 1,2, Yifan Mo 1,2, Michael Q. Zhang 2,3
1Department of Applied Mathematics & Statistics, Stony Brook University, 2Computational Biology and Bioinformatics, Cold Spring Harbor Laboratory, 3Department of Molecular and Cell Biology, University of Texas at Dallas

Our Bayesian Change Point (BCP) algorithm builds on state-of-the-art advances in modeling change-points via Hidden Markov Models and applies them to chromatin immunoprecipitation sequencing (ChIPseq) data analysis. BCP performs well in both broad and punctate data types, but excels in accurately identifying robust, reproducible islands of diffuse histone enrichment.

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Medicine

Live Imaging of Drug Responses in the Tumor Microenvironment in Mouse Models of Breast Cancer
Elizabeth S. Nakasone 1,2, Hanne A. Askautrud 2,3, Mikala Egeblad 2
1Watson School of Biological Sciences, 2Cold Spring Harbor Laboratory, 3Departments of Medical Genetics, University of Oslo and Oslo University Hospital

We describe a method for imaging response to anti-cancer treatment in vivo and at single cell resolution.

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Biology

A Strategy to Validate the Role of Callose-mediated Plasmodesmal Gating in the Tropic Response
Ritesh Kumar *1, Shu Wei Wu *1, Arya Bagus Boedi Iswanto 1, Dhinesh Kumar 1, Xiao Han 2, Jae-Yean Kim 1
1Division of Applied Life Science (BK21 plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, 2Biotechnology Research Institute, Chinese Academy of Agricultural Sciences

This article describes the methods for screening the genes controlling plasmodesmal permeability and hence auxin gradient during tropic response. This includes the measurement of the degree of tropic response in hypocotyl of Arabidopsis thaliana and checking plasmodesmal permeability by 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS) loading and finally callose level assessment.

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Neuroscience

Single-cell RNA Sequencing of Fluorescently Labeled Mouse Neurons Using Manual Sorting and Double In Vitro Transcription with Absolute Counts Sequencing (DIVA-Seq)
Anirban Paul 1, Z. Josh Huang 1
1Cold Spring Harbor Laboratory

This protocol describes the manual sorting procedure to isolate single fluorescently labeled neurons followed by in vitro transcription-based mRNA amplification for high-depth single-cell RNA sequencing.

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Genetics

A New Toolkit for Evaluating Gene Functions using Conditional Cas9 Stabilization
Polona Šafarič Tepeš 1,2, Raffaella Sordella 1
1Cold Spring Harbor Laboratory, 2Faculty of Pharmacy, University of Ljubljana

Here, we describe a genome-editing tool based on the temporal and conditional stabilization of clustered regularly interspaced short palindromic repeat- (CRISPR-) associated protein 9 (Cas9) under the small molecule, Shield-1. The method can be used for cultured cells and animal models.

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Cancer Research

Longitudinal Intravital Imaging Through Clear Silicone Windows
Laura Maiorino *1,2,3, Margaret Shevik *1,4,5, José M. Adrover 1, Xiao Han 1,6, Elias Georgas 7,8, John Erby Wilkinson 9, Harrison Seidner 1, Leonie Foerschner 1, David A. Tuveson 1, Yi-Xian Qin 8, Mikala Egeblad 1
1Cold Spring Harbor Laboratory, 2Cold Spring Harbor Laboratory School of Biological Sciences, 3Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 4Medical Scientist Training Program, School of Medicine, Stony Brook University, 5Graduate Program in Pharmacology, Stony Brook University, 6Graduate Program in Genetics, Stony Brook University, 7Graduate Program in Biomedical Engineering, Stony Brook University, 8Department of Biomedical Engineering, Stony Brook University, 9Department of Pathology, University of Michigan

An approach is here presented for long-term intravital imaging using optically clear, silicone windows that can be glued directly to the tissue/organ of interest and the skin. These windows are cheaper and more versatile than others currently used in the field, and the surgical insertion causes limited inflammation and distress to the animals.

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