.. _rna:

RNA Spot Data table
===================

Requirement level: optional

Recommended: **Yes**

Namespace: *4dn_FOF-CT_rna*

Summary
-------
This table is optionally used to store and share RNA Spot data that 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 **RNA_Spot_ID**, the **X**, **Y**, **Z** coordinates of each spot, the **Gene_ID**, the **RNA_name** 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 <https://doi.org/10.1073/pnas.1912459116>`_) 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 :ref:`demultiplexing` as described in the instructions of that table.

.. tip:: ``RNA_Spot_ID`` identifiers are unique across the entire dataset, thus allowing to identify unambiguously a Spot in the :ref:`quality`, :ref:`bio` and :ref:`demultiplexing`.

.. 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 :ref:`headers-reference-label`
- 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_mapping``.

.. tip:: 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 columns used.

.. csv-table::
  :file: tables/rna_header.csv
  :header-rows: 1

Data Columns
------------
- For full instructions see :ref:`columns-reference-label`

As with all other RNA Spot Data tables in this format, each row corresponds to data associated with an individual RNA_Spot.

The first columns are always: ``RNA_Spot_ID``, ``X``, ``Y``, ``Z``, ``RNA_name``, ``Gene_ID``, ``Trace_ID``, followed by ``Transcript_ID`` if applicable, and by **one or more** of the following ``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.

.. csv-table::
  :file: tables/rna_columns.csv
  :header-rows: 1
  
Example
-------
.. include:: examples/rna
  :code: