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IMPORTANT !!! This representation of FOF-CT is now deprecated and no longer maintained. Please refer to the ReadTheDocs page for any and all information about this format.
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Please refer to the ReadTheDocs page for any and all information about this format --> https://fish-omics-format.readthedocs.io/en/latest/
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Please report any questions, issues and proposals for change in the GitHub issue page --> https://github.com/4dn-dcic/fish_omics_format/issues
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Please refer to the ReadTheDocs page for any and all information about this format --> https://github.com/4dn-dcic/fish_omics_format/issues
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v0.1 FISH Omics Format - Chromatin Tracing
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Description:
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A key output of the 4DN project is the open publication of datasets related to the structure of the human cell nucleus and the genome, within. Recent years have seen a rapid expansion of FISH-omics methods, which quantify the spatial organization of DNA, RNA and protein in the cell and provide expanded understanding of how higher-order chromosome structure relates to transcriptional activity and cell development. Despite this progress, FISH-based image-data are not yet routinely made publicly available upon publication because of the lack of common specifications for data exchange. This challenge is experienced across the bioimaging community, as a result a solution built, tested and proven in 4DN can have a wide impact all over the world.

This document describes the 4DN FISH Omics Format - Chromatin Tracing (FOF-CT), a community data format designed for capturing and exchanging the results of chromosome imaging experiments produced within the context of the 4D Nucleome project. FOF-CT is directly compatible with several FISH omics techniques including, but not limited to, Optical Reconstruction of Chromatin Architecture (ORCA; https://doi.org/10.1038/s41596-020-00478-x), Multiplexed Imaging of Nucleome Architectures (MINA; https://doi.org/10.1038/s41596-021-00518-0), Hi-M (https://doi.org/10.1016/j.molcel.2019.01.011), DNA Sequential Fluorescence In Situ Hybridization (seqFISH+; https://doi.org/10.1038/s41586-019-1049-y), Oligonucleotide Fluorescent In Situ Sequencing (OligoFISSEQ; https://doi.org/10.1038/s41592-020-0890-0), DNA Multiplexed error-robust fluorescence in situ hybridization (DNA-MERFISH; https://doi.org/10.1016/j.cell.2020.07.032), and In-situ Genomic Sequencing (IGS; https://doi.org/10.1126/science.aay3446). In addition, the format is designed to be consistent with planned future extensions that will encompass single-molecule localization methods for volumetric imaging, such as OligoSTORM and OligoDNA-PAINT.

In chromatin tracing experiments, polymer tracing algorithms are used to string together the localization of individual DNA bright Spots to reconstruct the three-dimensional (3D) path of chromatin fibers. Thus, the format is organized around multiple tables. The core of the format consists of a Spot/Trace table that defines chromatin Traces as ensembles of individual DNA-FISH bright Spot localizations.

Additional tables support the integration of this core with additional properties such as quality metrics, physical coordinates placing the Spot/Trace in the context of cellular space, multiplexed RNA-FISH results (https://doi.org/10.1073/pnas.1912459116) and with additional data that is better captured at the global Trace (e.g., expression level of nascent RNA transcripts associated with a given Trace or overall localization of the Trace with respect to cellular or nuclear landmarks), Cell (e.g., boundaries and volume), sub-cellular Region of Interest (ROI), or extra-cellular ROI (e.g., Tissue) level.
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Overview
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The format is organized in multiple individual tables.
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The only mandatory table is the "DNA_Spot/Trace_Data_Table".
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All other tables are either recommended for all experiment types, or optional depending on the experiment design and type.
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Accepted file formats for storing Tables are txt, csv and tsv.
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Each file should contain a single Table.
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Each file has two parts:
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1File Header
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The file header contains required, conditionally-required, and optional fileds.
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Conditionally-required fields are fields that are required when certains conditions are met (e.g., ##intensity_unit= is required any time an intensity metric is reported).
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In addition conditionally-required header fields
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In the file header, each line contains only one field.
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Header names must use the underscore as a word separator (e.g., RNA_A_intensity).
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Header lines are denoted as follow:
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- ##denotes machine readable header lines. These lines must follow the following format, <Key1=Value1, Key2=Value2, etc.,> (e.g., '##FOF-CT_version=v0.1').
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- # denotes human readable header lines. These lines should follow the following format, <#term: free text description> (e.g., '#lab_name: name of the lab where the experiment was performed').
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- #^denotes lines that define optional user specified columns. These lines provide the name of the column header and a description of the column content. Descriptions must be understandable and sufficient to ensure the interpretation and reproducibility of the results. These lines should follow the following format, <#^term: free text description> format (e.g., '#^optional_column_1: optional column 1 description').
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Data columns
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Tables contain required, conditionally-required, and optional columns.
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Conditionally-required columns are columns that are required when certains conditions are met (e.g., Cell_ID is required any time the experiment involves the identification of Cell boundaries).
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Column names should use the underscore as a word separator (e.g., Spot_ID).
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The first column is always either Spot_ID or another relevant ID (i.e., Trace_ID, Cell_ID, etc.,). In the DNA_Spot/Trace_Data_Table, there are eight mandatory columns. All other columns are ordered at user's discretion.
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The order of the rows is at user's discretion.
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If an optional column does not contain any data (i.e., it is not used), it should be omitted.
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