Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of 2D vs 3D distance measurements in the analysis of various features of spatial genome organization. We find in general good agreement between 2D and 3D analysis with higher convergence of measurements as the interrogated distance increases, especially in flat cells. Overall, 3D distance measurements are more accurate than 2D distances, but are also more susceptible to noise. In particular, z-stacks are prone to error due to imaging properties such as limited resolution along the z-axis and optical aberrations, and we also find significant deviations from unimodal distance distributions caused by low sampling frequency in z. These deviations are ameliorated by significantly higher sampling frequency in the z-direction. We conclude that 2D distances are preferred for comparative analyses between cells, but 3D distances are preferred when comparing to theoretical models in large samples of cells. In general and for practical purposes, 2D distance measurements are preferable for many applications of analysis of spatial genome organization.

基因组的空间组织（spatial organization）并非随机分布，且具有细胞类型特异性，其与细胞功能紧密关联。传统上，对基因组空间组织的研究极大程度依赖荧光显微镜（fluorescence microscopy）技术。用于探究该空间组织的成像方法，其有效性往往取决于距离测量（distance measurements）的准确性与精度。基于成像的距离测量可分为两类：二维数据集，以及包含图像堆栈Z轴（z-axis）信息的三维数据集。本研究对比了二维与三维距离测量在分析基因组空间组织各类特征时的适用性。结果显示，总体而言二维与三维分析结果吻合度较好，且随着被测距离的增大，二者的收敛性更高，在扁平细胞中这一特征尤为显著。整体而言，三维距离测量的精度高于二维距离测量，但更易受噪声干扰。具体而言，Z轴方向有限的分辨率与光学像差等成像特性，会导致Z堆栈（z-stacks）产生误差；此外我们还发现，Z方向采样频率过低会引发与单峰距离分布（unimodal distance distributions）显著偏离的情况。通过提高Z方向的采样频率，可显著缓解此类偏差。我们得出结论：在细胞间的比较分析中，优先选用二维距离测量；而在大量细胞样本中与理论模型进行对比时，则优先选用三维距离测量。总体而言，出于实践考量，二维距离测量在基因组空间组织分析的诸多应用场景中更为适用。