RNA-Spot Data table
Requirement level: conditionally required
Summary
This table is used to store and share the results of RNA FISH-omics experiments and it is conditionally required in the case RNA data was collected as part of this experiment. Each row represents a detected RNA bright Spot and corresponds to the location of a specific RNA transcript.
At a minimum, one needs to know the Spot_ID, the X, Y, Z coordinates of each spot, the Gene_ID and an additional ID used to link this data with other tables in this format (i.e., Trace_ID, Sub_Cell_ROI_ID, Cell_ID and/or Extra_Cell_ROI_ID). In addition, in case multiple transcripts are associated with the same Gene_ID and the FISH probes are capable of distinguishing them, Transcript_ID MUST also be reported. Thus, at a minimum there needs to be 6 (or 7) data columns. These are required. All other data columns are optional.
In this table the reported X, Y and Z coordinates are assumed to result from post-processing and quality control procedures performed on primary localization events and therefore correspond to what is considered the best-bet location of the RNA molecule under study.
In the case of multiplexed FISH experiments (i.e., MERFISH) in which the final location of RNA molecule results from combining multiple detection events (e.g., by combining individual Localization events detected in separate planes or images), the underlying raw data can be recorded in the corresponding Spot Demultiplexing table as described in the instructions of that table.
Spot_ID identifiers are unique across the entire dataset, thus
allowing to identify unambiguously a Spot in the Spot Quality table, Spot Biological Data table and
Spot Demultiplexing table.
NOTE: Also DNA Spots have a `Spot_ID (in the DNA-Spot/Trace Data core table). Thus, when
assigning an identifier to each Spot, make sure that this is unique not only
within the RNA-Spot Data table, but also in the DNA-Spot/Trace Data core table.
Example
##FOF-CT_version=v0.1
##Table_namespace=4dn_FOF-CT_rna
##genome_assembly=GRCh38
##XYZ_unit=micron
##Gene_ID_type=Ensemble_V38
#Software_Title: Xyz
#Software_Type: SpotLoc
#Software_Authors: Janet Doette
#Software_Description: Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sagittis est mollis, pulvinar tortor mattis, dignissim nisi. Nunc tincidunt volutpat lacus vitae bibendum.
#Software_Repository: https://xyz.com
#Software_PreferredCitationID: https://doi.org/xyz
#lab_name: Nobel
#experimenter_name: John Doe
#experimenter_contact: john.doe@email.com
#additional_tables: 4dn_FOF-CT_core, 4dn_FOF-CT_quality, 4dn_FOF-CT_cell
##columns=(Spot_ID, X, Y, Z, RNA_name, Gene_ID, Transcript_ID, Cell_ID)
1, 14.43, 41.43, 1.23, ACTB, ENSG00000075624, ENST00000646664.1, 1
2, 14.83, 41.83, 1.83, GAPDH, ENSG00000111640, ENST00000229239.10, 1
3, 15.83, 42.83, 1.33, MB, ENSG00000198125, ENST00000397326.7, 1
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_rna”
The header MUST contain a mandatory set of fields that describe the algorithm(s) that were used to identify and localize bright Spots. In case more than one algorithm were used, please use the same set of fields for each of them.
The header MUST include a detailed description of each optional columns used.
Name |
Description |
Example |
Conditional requirement conditions |
|---|---|---|---|
##FOF-CT_version= |
Version of the FOF format used in this case. |
v0.1 |
|
##Table_namespace= |
Identifier for this type of table. Value must be as in the example. |
4dn_FOF-CT_rna |
|
#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(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces. |
ChrTracer3 |
|
#Software_Type: |
The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other |
SpotLoc+Tracing |
|
#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,. |
Mateo, LJ; Sinnott-Armstrong, N; Boettiger, AN |
|
#Software_Description: |
A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility. |
ChrTracer3 software was developed for analysis of raw DNA labeled images. As an input, it takes an.xlsx table containing information and folder names of the DNA experiment. As an output, it returns tab delimited.txt files with drift-corrected x, y, z positions for all labeled barcodes. These can be used directly to calculate the nm scale distances between all pairs of labeled loci. The current version of the software as of this writing is ChrTracer3. |
|
#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,. |
||
#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_quality, 4dn_FOF-CT_bio, 4dn_FOF-CT_trace, 4dn_FOF-CT_cell |
|
##genome_assembly= |
Genome build. Note: the 4DN Data Portal only accepts GRCh38 for human and GRCm38 for mouse. |
GRCh38 |
|
##Gene_ID_type= |
The field used to report the type of unique ID used to identify the Gene encoding for the targeted RNA transcript. |
Ensemble_V38 |
|
##Transcript_ID_type= |
The field used to report the type of unique ID used to identify the targeted RNA transcript. |
Ensemble_V38 |
Conditional requirement: this MUST be reported if multiple transcripts are associated with the same Gene_ID and the FISH probes are capable of distinguishing them. |
##XYZ_unit= |
The unit used to represent XYZ location of bright Spots in this table. Note: use micron (instead of µm) to avoid problem with special, Greek symbols. Other allowed values are: nm, mm etc. |
micron |
|
##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, X, Y, Z) |
Data Columns
As with all other Spot Data tables in this format, each row corresponds to data associated with an individual Spot.
The first columns are always: Spot_ID, X, Y, Z, RNA_name, Gene_ID, followed by Transcript_ID if applicable, and by one or more of the following Trace_ID, Sub-Cell_ROI_ID, Cell_ID and/or Extra_Cell_ROI_ID. 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 |
|
X |
The sub-pixel X coordinate of this bright Spot. NOTE: the reported X position is understood to be the one resulting from any performed post-processing procedures (i.e. drift correction, chromatic correction etc). |
14.43 |
|
Y |
The sub-pixel Y coordinate of this bright Spot. NOTE: the reported Y position is understood to be the one resulting from any performed post-processing procedures (i.e. drift correction, chromatic correction etc). |
14.43 |
|
Z |
The sub-pixel Z coordinate of this bright Spot. NOTE: the reported Z position is understood to be the one resulting from any performed post-processing procedures (i.e. drift correction, chromatic correction etc). |
1.23 |
|
RNA_name |
This is the official name of the Gene the targeted RNA is transcribed from. |
ACTB |
|
Gene_ID |
This is the official ID for the Gene encoding for the targeted RNA transcript. |
ENSG00000075624 |
|
Transcript_ID |
This is the official ID for the targeted RNA transcript. This field is required in case the same Gene has multiple different Transcripts and the FISH probe used in this case is capable of distinguishing between them. |
ENST00000646664.1 |
Conditional requirement: this MUST be reported if multiple transcripts are associated with the same Gene_ID and the FISH probes are capable of distinguishing them. |
Trace_ID |
This fields reports the unique identifier for a DNA Trace identified as part of this experiment. Note: this is used to connect data in this table with a given Trace and with Trace specific measurements as recorded in the corresponding Trace Data table. |
1 |
Conditional requirement: this column is mandatory if data in this table can be associated with a Trace identified as part of this experiment. |
Sub_Cell_ROI_ID |
If known, this fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a sub-cellular structure a given Spot is associated with. Note: this is used to connect individual Spots that are part of the same ROI. It is also used to connect data in this table with any ROI specific measurements such as boundaries, intensities or volume, recorded in the corresponding Sub-Cell ROI Data table. |
1 |
Conditional requirement: this column is mandatory if data in this table can be associated with a Sub_Cell_ROI identified as part of this experiment. |
Cell_ID |
If known, this fields reports the unique identifier for the Cell a given Spot is associated with. Note: this is used to connect individual Spots that are part of the same Cell. It is also used to connect data in this table with any Cell specific measurements such as boundaries, intensities and volume, recorded in the corresponding Cell Data table. |
1 |
Conditional requirement: this column is mandatory if data in this table can be associated with a Cell identified as part of this experiment. |
Extra_Cell_ROI_ID |
If known, this fields reports the unique identifier for a Region of Interest (ROI) that represents the boundaries of a extracellular structure (e.g., Tissue) a given Spot is associated with. Note: this is used to connect individual Spots that are part of the same ROI. It is also used to connect data in this table with any ROI specific measurements such as boundaries, intensities and volume, recorded in the corresponding Extra-Cell ROI Data table. |
1 |
Conditional requirement: this column is mandatory if data in this table can be associated with a extracellular structure ROI (e.g., Tissue) identified as part of this experiment. |