GeoMx Level 3
A NanoString GeoMx Level 3 entry documents the fully processed count data produced by the NanoString GeoMx DSP pipeline, such as final probe- or target-level expression matrices. This level captures the unique probe and unique target counts represented in the file, the matrix type (e.g. raw, normalized, or background-subtracted counts), and the software, workflow, and parameters used to generate the processed output, including a link to the workflow for reproducibility.
Level 3 entries represent the analysis-ready data products most commonly used for downstream statistical analysis, while still preserving a clear lineage back to the Level 2 count conversion and Level 1 raw reads that produced them.
Why You Should Contribute NanoString GeoMx Level 3 Entries¶
Contributing Level 3 entries ensures that processed count data is documented with enough workflow and provenance detail for others to understand exactly how it was derived, and to confidently reuse it in downstream analyses shared through the CCKP.
Who Should Be Contributing NanoString GeoMx Level 3 Entries?¶
- Computational Analysts – Document the workflow, parameters, and matrix type used to generate processed count data.
- Bioinformatics Pipeline Developers – Record the software and workflow versions that produced the processed outputs, supporting reproducibility.
- Spatial Biology Researchers – Track which processed data products correspond to which raw reads and ROI/segments.
- Data Managers – Maintain consistent, portal-ready metadata for processed GeoMx outputs shared through the CCKP.
Download Template¶
You can download the NanoStringGeoMxDSPLevel3 CSV template to streamline data entry.
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | Examples |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMxDSPLevel3_id | Unique row identifier, used as a primary key for record updates. This should be equivalent to the file Synapse Id unless otherwise indicated. | True | string | None | ^syn\d{7,8}$ | None | |
| Filename | The path of a file in Synapse, relative to the project. The file associated with the path will be annotated with attributes contained in this sheet. | False | string | None | None | None | |
| NanoStringGeoMxDSPLevel1 Key | Unique NanoStringGeoMxDSPLevel1_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| NanoStringGeoMxDSPLevel2 Key | Unique NanoStringGeoMxDSPLevel2_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| NanoStringGeoMxAuxiliaryFiles Key | Unique NanoStringGeoMxAuxiliaryFiles_id foreign key(s) that link metadata entries as part of the same Dataset. Please provide multiple values as a comma-separate list. | False | string | None | None | None | |
| Biospecimen Key | Unique Biospecimen_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | -B\d{1,9} | None | |
| Study Key | The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| DatasetView Key | Unique DatasetView_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list. | False | string | None | None | None | |
| File Alias | A string identifier associated with the file. Must be unique. Can be the repository accesssion number (e.g., Synapse ID, GEO identifier such as GSE12345). No Greek Letters or DOIs. | True | string | None | None | None | |
| File Description | Description of the file. | False | string | None | None | None | |
| File Design | The overall design of the dataset or file, including a batch identifier, if applicable. | False | string | None | None | None | |
| File Level | The processing level the file can be mapped to. | True | string | None | None | View | |
| File Assay | The assay the file is representative of. | True | string | None | None | View | |
| File Species | The species the data was collected on. | True | string | None | None | View | |
| File Url | The url of where the file is stored. | True | string | uri | None | None | |
| File Format | The format of the file described by this entry. | True | string | None | None | View | |
| File Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/study/#attribute-study-data-use-codes | False | string_list | None | None | None | |
| File Longitudinal Group | A label that can be used to identify groups of files from the same longitudinal/time-resolved experiment | False | string | None | None | None | |
| File Longitudinal Event Type | The type of event to which File Longitudinal Total Time Elapsed is related | False | string | None | None | View | |
| File Longitudinal Sequence Identifier | The order in which this file was collected with respect to the longitudinal experiment (e.g., 1, 2, etc.). Integer. | False | number | None | None | None | |
| File Longitudinal Time Elapsed Unit | The unit of time associated with Sequential and Total Time Elapsed attributes. | False | string | None | None | None | |
| File Longitudinal Total Time Elapsed | The total time elapsed between the first and current files contained this longitudinal group. | False | number | None | None | None | |
| NGS Unique Probe Count | Total number of unique probes reported. | False | number | None | None | None | |
| NGS Unique Target Count | Total number of unique genes reported. | False | number | None | None | None | |
| NGS Matrix Type | Type of count data stored in matrix. | False | string | None | None | View | |
| Software and Version | Name of software used to generate the information contained in the file. String | False | string | None | None | None | |
| Workflow Type | Type of computational workflow used to generate the file. | False | string | None | None | None | |
| Workflow Parameter Description | Link or text description of flags or options provided to the workflow used to generate the file. | False | string | None | None | None | |
| Workflow Link | Link to documentation or webpage associated with the computational workflow used to generate the file. | False | string | uri | None | None |