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In situ genome sequencing resolves DNA sequence and structure in intact biological samples.

Science (New York, N.Y.) (2021-01-02)
Andrew C Payne, Zachary D Chiang, Paul L Reginato, Sarah M Mangiameli, Evan M Murray, Chun-Chen Yao, Styliani Markoulaki, Andrew S Earl, Ajay S Labade, Rudolf Jaenisch, George M Church, Edward S Boyden, Jason D Buenrostro, Fei Chen

Understanding genome organization requires integration of DNA sequence and three-dimensional spatial context; however, existing genome-wide methods lack either base pair sequence resolution or direct spatial localization. Here, we describe in situ genome sequencing (IGS), a method for simultaneously sequencing and imaging genomes within intact biological samples. We applied IGS to human fibroblasts and early mouse embryos, spatially localizing thousands of genomic loci in individual nuclei. Using these data, we characterized parent-specific changes in genome structure across embryonic stages, revealed single-cell chromatin domains in zygotes, and uncovered epigenetic memory of global chromosome positioning within individual embryos. These results demonstrate how IGS can directly connect sequence and structure across length scales from single base pairs to whole organisms.

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Triton X-100 solution, BioUltra, for molecular biology, ~10% in H2O
Glucose Oxidase from Aspergillus niger, Type VII, lyophilized powder, ≥100,000 units/g solid (without added oxygen)
3-(Trimethoxysilyl)propyl methacrylate, 98%
Ammonium persulfate, for molecular biology, suitable for electrophoresis, ≥98%
Triton X-100, laboratory grade
(±)-6-Hydroxy-2,5,7,8-tetramethylchromane-2-carboxylic acid, 97%
(+)-N,N′-Diallyltartramide, ≥99%
M2 medium, With HEPES, without penicillin and streptomycin, liquid, sterile-filtered, suitable for mouse embryo cell culture
N,N,N′,N′-Tetramethylethylenediamine, BioReagent, for molecular biology, ≥99% (GC)
Flow Cup Viscosity Standard, UKAS ISO/IEC17025 and ISO 17034 certified, viscosity 281.4 mPa.s (20 °C)