GeoMx Level 1
A NanoString GeoMx Level 1 entry describes the raw sequencing files produced from a GeoMx Digital Spatial Profiler (DSP) experiment, prior to alignment or count conversion. This includes the assay type used in the DSP pipeline (RNA or Protein, run via nCounter or NGS) along with detailed next-generation sequencing (NGS) library metadata: library strategy, source material and molecule, selection method, layout, sequencing platform, read length, raw read counts, unique bases, sequencing coverage, and the library preparation kit name, vendor, and version.
Level 1 entries represent the earliest and most complete record of what was sequenced during a GeoMx run, and they anchor the full data provenance chain — every downstream processed file (Level 2 count conversions and Level 3 processed counts) traces back to the raw reads documented here.
Why You Should Contribute NanoString GeoMx Level 1 Entries¶
Contributing Level 1 entries ensures that raw GeoMx sequencing outputs are properly cataloged with the library preparation and sequencing details needed to interpret them, and are traceable back to the biospecimen and ROI/segment they were derived from.
Who Should Be Contributing NanoString GeoMx Level 1 Entries?¶
- Core Facility Staff – Document the library preparation kit, sequencing platform, and run parameters used to generate raw reads.
- Spatial Biology Researchers – Confirm that raw sequencing files are correctly linked to the biospecimen and segments profiled.
- Computational Analysts – Ensure sequencing metadata is complete so raw files can be correctly processed into Level 2 and Level 3 outputs.
- Data Managers – Track raw sequencing files as they are deposited to ensure completeness of the GeoMx data provenance chain.
Download Template¶
You can download the NanoStringGeoMxDSPLevel1 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 |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMxDSPLevel1_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 | |
| 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 | |
| NanoStringGeoMXROISegmentAnnotation Key | Unique NanoStringGeoMXROISegmentAnnotation_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 | |
| GeoMx DSP Assay Type | The assay type which was used for the GeoMx DSP pipeline. | False | string | None | None | View | |
| NGS Library Strategy | The assay associated with the nucleic acid library (e.g., RNA-Seq, ChIP-Seq) | True | string | None | None | View | |
| NGS Library Source Material | The type of source material being sequenced. | True | string | None | None | View | |
| NGS Library Source Molecule | The source of nucleic acids represented in the sequencing library. | True | string | None | None | View | |
| NGS Library Selection Method | How nucleic acid molecules are isolated. | False | string | None | None | View | |
| NGS Library Layout | Text description of the library layout, one of Paired-end or Single. | True | string | None | None | View | |
| NGS Sequencing Platform | A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument. | True | string | None | None | View | |
| NGS Sequencing Design Description | Free-form description of the methods used to create the sequencing library; a brief 'materials and methods' section. | True | string | None | None | None | |
| NGS Read Length | The average length of the sequencing reads. Can be integer, null | True | number | None | None | None | |
| NGS Raw Reads | Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file. | False | number | None | None | None | |
| NGS Unique Bases | Count of unique basecalls present in the data. | False | number | None | None | None | |
| NGS Sequencing Coverage | Depth of coverage on assembly used. Found by (Unique Aligned Basecalls)/(Reference Length) | False | number | None | None | None | |
| NGS Library Preparation Kit Name | Name of Library Preparation Kit. String | False | string | None | None | None | |
| NGS Library Preparation Kit Vendor | Vendor of Library Preparation Kit. String | False | string | None | None | None | |
| NGS Library Preparation Kit Version | Version of Library Preparation Kit. String | False | string | None | None | None | |
| NGS Read Indicator | Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads (I1), or Other | True | string | None | None | View | |
| NGS Library Preparation Days from Index | Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable' | False | string | None | \d+$|Not\sApplicable$|unknown$ | None | |
| NGS Sequencing Library Construction Days from Index | Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable' | True | string | None | \d+$|Not\sApplicable$|unknown$ | None |