Navelkar Rahi, Cosolo Andrea, Bintu Bogdan, Cheng Yubao, Gardeux Vincent, Gutnik Silvia, Fujimori Taihei, Hafner Antonina, Jay Atishay, Jia Bojing Blair, Jussila Adam Paul, Llimos Gerard, Lioutas Antonios, Martins Nuno M C, Moore William J, Takei Yodai, Wong Frances, Yang Kaifu, Zhang Huaiying, Zhu Quan, Bienko Magda, Bintu Lacramioara, Cai Long, Deplancke Bart, Nollmann Marcelo, Mango Susan E, Ren Bing, Park Peter J, Sawh Ahilya N, Schroeder Andrew, Swedlow Jason R, Vahedi Golnaz, Wu Chao-Ting, Aufmkolk Sarah, Boettiger Alistair N, Farabella Irene, Strambio-De-Castillia Caterina, Wang Siyuan
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Shu Chien-Gene Lay, Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
ArXiv. 2025 Aug 21:arXiv:2508.13255v2.
A key output of the NIH-Common Fund 4D Nucleome (4DN) project is the open publication of datasets related to the structure of the human cell nucleus and the genome. Recent years have seen a rapid expansion of multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods, which quantify the spatial organization of chromatin in single cells, sometimes together with RNA and protein measurements, and provide an expanded understanding of how 3D higher-order chromosome structure relates to transcriptional activity and cell development in both health and disease. Despite this progress, results from Chromatin Tracing FISH-omics experiments are difficult to share, reuse, and subject to third-party downstream analysis due to the lack of standard specifications for data exchange. Following up on the recent publication of Microscopy Metadata specifications , we present the 4DN FISH Omics Format - Chromatin Tracing (FOF-CT), a community-developed data standard for processed results derived from a wide variety of imaging techniques for Chromatin Tracing, with the most recent studies falling roughly into two categories: ball-and-stick and volumetric based on whether they represent the targeted genomic segment as individual fluorescence spots or as clouds of single-molecule localizations. To demonstrate the value and potential use of FOF-CT to promote the FAIR sharing of the results obtained from Chromatin Tracing techniques, this manuscript will focus on ball-and-stick Chromatin Tracing techniques, including those described by the pioneering Chromatin Tracing study of Wang et al. as well as Optical Reconstruction of Chromatin Architecture (ORCA) , microscopy-based chromosome conformation capture (Hi-M) , Multiplexed Imaging of Nucleome Architectures (MINA) , DNA Sequential Fluorescence In Situ Hybridization (DNA seqFISH/seqFISH+) , Oligopaint Fluorescent In Situ Sequencing (OligoFISSEQ) , DNA Multiplexed error-robust fluorescence in situ hybridization (DNA-MERFISH) , and In-situ Genomic Sequencing (IGS) . The manuscript will describe the structure of the format and present a collection of FOF-CT datasets that were recently deposited to the 4DN Data Portal and the Open Microscopy Environment (OME) Image Data Resource (IDR) platform and are ideally suited for promoting reuse, exchange, further processing, and integrative modeling. Furthermore, the manuscript will present examples of analysis pipelines that could be applied more widely due to the existence of the FOF-CT exchange data format and provide examples of biological conclusions that could be drawn thanks to the availability of such datasets.
美国国立卫生研究院共同基金4D细胞核组（4DN）项目的一项关键成果是公开与人类细胞核和基因组结构相关的数据集。近年来，多重荧光原位杂交（FISH）或FISH组学方法迅速发展，这些方法可量化单细胞中染色质的空间组织，有时还结合RNA和蛋白质测量，从而更深入地了解三维高阶染色体结构在健康和疾病状态下与转录活性及细胞发育的关系。尽管取得了这一进展，但由于缺乏数据交换的标准规范，染色质追踪FISH组学实验的结果难以共享、重复使用，也难以进行第三方下游分析。继显微镜元数据规范最近发布之后，我们推出了4DN FISH组学格式 - 染色质追踪（FOF-CT），这是一种由社区开发的数据标准，用于处理源自多种染色质追踪成像技术的结果，最近的研究大致可分为两类：基于球棒模型和基于体积模型，这取决于它们将目标基因组片段表示为单个荧光点还是单分子定位云。为了证明FOF-CT在促进染色质追踪技术所得结果的公平共享方面的价值和潜在用途，本手稿将重点关注基于球棒模型的染色质追踪技术，包括Wang等人开创性的染色质追踪研究 以及染色质结构光学重建（ORCA） 、基于显微镜的染色体构象捕获（Hi-M） 、细胞核组结构多重成像（MINA） 、DNA序列荧光原位杂交（DNA seqFISH/seqFISH+） 、寡核苷酸荧光原位测序（OligoFISSEQ） 、DNA多重误差稳健荧光原位杂交（DNA-MERFISH） 和原位基因组测序（IGS） 中描述的技术。本手稿将描述该格式的结构，并展示一组最近存入4DN数据门户 和开放显微镜环境（OME）图像数据资源（IDR）平台的FOF-CT数据集，这些数据集非常适合促进重复使用、交换、进一步处理和整合建模。此外，本手稿将给出一些分析流程的示例，由于FOF-CT交换数据格式的存在，这些流程可以更广泛地应用，并给出借助此类数据集可以得出的生物学结论的示例。
