Spot Biological Data table
Requirement level: optional
Recommended: Yes
Namespace: 4dn_FOF-CT_bio
Summary
This table is highly recommended and it is designed to store and share biological properties associated with individual Spots (e.g., distance from the nuclear lamina (NL) or the nuclear pore complex (NPC), etc.; Su et al 2020 Cell and Takei et al 2021 Nature) identified as part of this experiment. In the absence of a consensus regarding biological properties to be recorded in association with individual bright Spots, the specific columns in this table remain at the user’s discretion and should be described with sufficient details to ensure interpretation and reproducibility.
This table is mandatorily indexed by Spot_ID.
Warning
All MANDATORY header fields and column names are indicated in bold. All conditionally required header fields and column names are indicated in italics.
File Header
For full instructions see File Header
The first line in the header is always
##FOF-CT_Version=vX.X.The second line in the header is always
##Table_Namespace=4dn_FOF-CT_bio.
Tip
If applicable, the header MUST contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
The header MUST include a detailed description of each Optional Column used.
Tip
The table MUST contain at least 1 Optional Column.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
##FOF-CT_Version= |
Version of the FOF format used in this case. |
v2.0 |
|
##Table_Namespace= |
Identifier for this type of table. Value must be as in the example. |
4dn_FOF-CT_bio |
|
##XYZ_Unit= |
The unit used to represent XYZ locations or distances in this table. Note: use micron to avoid problems with special, Greek symbols. Allowed values (closed list): ‘nm’, ‘micron’, ‘mm’. |
micron |
|
##Time_Unit= |
If relevant, the unit used to represent a time interval in this table. Allowed values (closed list): ‘ms’, ‘msec’, ‘s’, ‘sec’, ‘min’, ‘hr’. |
sec |
Conditional requirement (Metric-triggered, see Conditional Requirements Reference): MUST be reported if any time metric is reported in an optional column of this table. |
##Intensity_Unit= |
The unit used to represent intensity measurements in this table. |
a.u. |
Conditional requirement (Metric-triggered, see Conditional Requirements Reference): MUST be reported if any intensity metric is reported in an optional column of this table. |
#Lab_Name: |
name of the lab where the experiment was performed. |
Nobel |
|
#Experimenter_Name: |
name of the person performing the experiment. |
John Doe |
|
#Experimenter_Contact: |
email address of the person performing the experiment. |
||
#Description: |
A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#Software_Title: |
The name of the Software tool that was used to produce the results reported in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them. |
AlgorithmXYZ |
|
#Software_Type: |
The type of this Software used to produce results recorded in this table. Allowed values: Distance Calculation, DriftCorrection, Precision Assessment, Segmentation, Single Molecule Localization, SpotLoc, SpotLoc+Tracing, Tracing, Other |
Segmentation |
|
#Software_Authors: |
The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,. |
John Doe |
|
#Software_Description: |
A free-text, description of this Software. This description should provide a detailed understanding of the algorithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility. |
A pretty clear description |
|
#Software_Parameters: |
A free-text description of the input parameters used for the specific analysis run performed using this Software. This description should provide sufficient details about the analysis parameters that were used as to guarantee interpretation and reproducibility. Example include input parameter used for assessing the precision of single molecule localization or drift correction in X, Y and Z. |
X_Loc_Precision Parameter = 1.01 |
|
#Software_Repository: |
The URL of any repository or archive where the Software executable release can be obtained. |
||
#Software_PreferredCitationID: |
The Unique Identifier for the preferred/primary publication describing this Software. Examples include Digital Object Identifier (DOI), PubMed Central Identifier (PMCID), ArXiv.org ID etc. |
||
#Intensity_Measurement_Method |
The method that was used to perform intensity measurements. In particular, sufficient information should be provided to document how digital intensity signals were converted to Photon counts. |
Mean Fluorescence Intensity |
Conditional requirement (Metric-triggered, see Conditional Requirements Reference): MUST be reported if any intensity metric is reported in an optional column of this table. |
#^Optional_Column_1: |
Optional column 1 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
Conditional requirement (Structural — at least one Optional_Column required, see Conditional Requirements Reference): this table MUST contain at least 1 Optional Column. |
|
#^Optional_Column_2: |
Optional column 2 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#^Optional_Column_3: |
Optional column 3 description. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility. |
||
#Additional_Tables: |
list of the additional tables being submitted. Note: use a comma to separate each table name from the next. |
4dn_FOF-CT_core, 4dn_FOF-CT_rna, 4dn_FOF-CT_quality, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell |
|
##Columns= |
list of the data column headers used in the table. Note: enclose the column headers and use a comma to separate each header name from the next. |
(Spot_ID, Optional_column_1, Optional_column_2, Optional_colummn_3, …) |
Data Columns
For full instructions see Data Columns
Each row corresponds to data associated with an individual Spot.
The first column is always Spot_ID.
This table MUST contain at least 1 Optional Column.
The order of the other columns is at user’s discretion.
The order of the rows is at user’s discretion.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
Spot_ID |
A unique identifier for this bright Spot. |
1 |
|
Optional_Column_1 |
|||
Optional_Column_2 |
|||
Optional_Column_3 |
Example
The only mandatory column in this table is Spot_ID. All other columns are optional and must be defined by the user using a Header line starting with #^.
Tip
The optional columns in this example table are included for illustrative purposes only and describe a case in which the user is reporting the distance of DNA spots from two different nuclear landmarks.
##FOF-CT_Version=v2.0
##Table_Namespace=4dn_FOF-CT_bio
##XYZ_Unit=micron
#Lab_Name: Nobel
#Experimenter_Name: John Doe
#Experimenter_Contact: john.doe@email.com
#Description: In this experiment the nuclear location of DNA Bright Spots was mapped with respect to the Nuclear Lamina (NL) and the location of the nearest H4K27me3 signal.
#Software_Title: AlgorithmXYZ
#Software_Type: Distance Calculation
#Software_Authors: John Doe
#Software_Description: A pretty clear description
#Software_Parameters: Minimum object size = 10 pixel, X-Y-Z Loc_Precision Parameter = 1.01
#Software_Repository: https://github.com/repo_name_goes_here
#Software_PreferredCitationID: https://doi.org/doi_goes_here
#^NL_Distance: the Euclidean 3D distance between the centroid of the indicated DNA Spot and the Nuclear Lamina identified using the convex hull surrounding all detected chromatin loci, as described in Doe et al., 2021.
#^H4K27me3_Distance: the Euclidean 3D distance between the centroids of the indicated DNA Spot and the closest H4K27me3 signal, respectively. H4K27me3 enriched chromatin was detected using the XYZ antibody as described in Doe et al, 2021.
#Additional_Tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_demultiplexing, 4dn_FOF-CT_trace, 4dn_FOF-CT_rna
##Columns=(Spot_ID, NL_Distance, H4K27me3_Distance)
1, 1.345, 0.445
2, 1.245, 0.005
3, 1.005, 0.150