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Sequencing Level 3

A Sequencing Level 3 entry documents further-processed sequencing data derived from a Sequencing Level 2 alignment, such as count matrices or probe-level summaries. This level captures matrix-type metadata (raw, normalized, scaled, or batch-corrected counts), unique probe and target counts, and the workflow, software, and parameters used to generate the processed output.

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 alignment and Level 1 raw reads that produced them.

Why You Should Contribute Sequencing Level 3 Entries

Contributing Sequencing 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 Sequencing Level 3 Entries?

  1. Computational Genomics Analysts – Document the workflow, parameters, and matrix type used to generate processed count data.
  2. Bioinformatics Pipeline Developers – Record the software and workflow versions that produced the processed outputs, supporting reproducibility.
  3. Research Staff – Track which processed data products correspond to which raw and aligned files.
  4. Data Managers – Maintain consistent, portal-ready metadata for processed sequencing outputs shared through the CCKP.

Download Template

You can download the SequencingLevel3 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
SequencingLevel3_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
SequencingLevel2 Key Unique SequencingLevel2_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
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
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