GeoMx Level 2
A NanoString GeoMx Level 2 entry documents processed count conversion files (DCC/RCC) derived from a GeoMx Level 1 raw sequencing file. This level captures the same core library preparation and sequencing platform metadata as Level 1, along with the read-processing metrics generated during count conversion: stitched reads, aligned reads, deduplicated reads, trimmed reads, percent reads mapping at Q30 (MapQ30), unique bases, sequencing coverage, the genomic reference used, and the software and version that performed the conversion.
Level 2 entries represent the intermediate step between raw sequencing reads and analysis-ready processed counts, preserving a clear lineage back to the Level 1 raw reads that produced them while capturing the alignment and deduplication metrics needed to assess data quality.
Why You Should Contribute NanoString GeoMx Level 2 Entries¶
Contributing Level 2 entries ensures that the read-processing and alignment steps between raw reads and final count data are documented with enough detail for others to assess data quality and trace processed counts back to their source reads.
Who Should Be Contributing NanoString GeoMx Level 2 Entries?¶
- Computational Analysts – Document the software, genomic reference, and alignment/deduplication metrics used to generate count conversion files.
- Core Facility Staff – Provide the sequencing platform and library details carried through from Level 1.
- Bioinformatics Pipeline Developers – Record workflow and software versions to support reproducibility of the count conversion step.
- Data Managers – Maintain consistent, portal-ready metadata linking Level 1 raw reads to Level 2 processed outputs.
Download Template¶
You can download the NanoStringGeoMxDSPLevel2 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 |
|---|---|---|---|---|---|---|---|
| NanoStringGeoMxDSPLevel2_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 | |
| 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 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 Stitched Reads | Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads | False | number | None | None | None | |
| NGS Aligned Reads | Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets. | False | number | None | None | None | |
| NGS Deduplicated Reads | Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data. | False | number | None | None | None | |
| NGS Trimmed Reads | Number of the reads remaining after trimming has been applied. | False | number | None | None | None | |
| NGS MapQ30 | Number of reads with Quality >= 30. | False | number | None | None | None | |
| NGS Unique Bases | Count of unique basecalls present in the data. | False | number | None | None | None | |
| NGS Read Length | The average length of the sequencing reads. Can be integer, null | True | 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 | |
| Genomic Reference | Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39) | False | string | None | None | None | |
| Software and Version | Name of software used to generate the information contained in the file. String | False | string | None | None | None |