Visium RNA Level 1
A 10x Visium RNA Level 1 entry documents raw RNA sequencing data associated with a Visium spatial transcriptomics spot/slide experiment. In addition to standard NGS library and platform fields, this level captures Visium-specific slide and library metadata, including the Visium run ID, spatial read content (spatial barcode and UMI vs. cDNA), spatial library construction method, capture area, slide version and ID, image re-orientation, and permeabilization time, along with RNA quality metrics such as RIN and DV200.
Because Visium data links sequencing reads to a specific physical location on a slide, accurate capture of the slide, capture area, and read-structure metadata at this level is essential for correctly reconstructing the spatial context of the data in downstream processing.
Why You Should Contribute 10x Visium RNA Level 1 Entries¶
Contributing 10x Visium RNA Level 1 entries ensures that raw spatial sequencing reads are documented with the slide, capture area, and library metadata needed to correctly reconstruct spatial context in downstream alignment and analysis shared through the CCKP.
Who Should Be Contributing 10x Visium RNA Level 1 Entries?¶
- Spatial Biology Researchers – Record slide, capture area, and permeabilization details from the Visium experiment.
- Sequencing Core Staff – Capture library preparation and platform metadata for the spatial sequencing run.
- Computational Genomics Analysts – Ensure raw file and slide metadata is complete before spatial alignment pipelines are run.
- Data Managers – Maintain consistent, portal-ready metadata for raw Visium sequencing outputs shared through the CCKP.
Download Template¶
You can download the VisiumRNALevel1 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 |
|---|---|---|---|---|---|---|---|
| 10xVisiumRNALevel1_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 | |
| 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 | |
| Visium Run ID | A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow. | True | 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 | |
| Visium Spatial Read1 | Read 1 content description | True | string | None | None | View | |
| Visium Spatial Read2 | Read 2 content description | True | string | None | None | View | |
| Visium Spatial Library Construction Method | Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711] | 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 | |
| NGS RNA End Bias | The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript | True | string | None | None | View | |
| NGS RNA Reverse Transcription Primer | An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA | 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 | |
| Visium Capture Area | Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1. | False | string | None | None | View | |
| Image Protocol Link | Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated. | False | string | uri | None | None | |
| Visium Slide Version | Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts. | True | string | None | None | View | |
| Visium Slide ID | For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide. | True | string | None | None | None | |
| Visium Image Re-orientation | To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation. | False | boolean | None | None | View | |
| Visium Permeabilization Time | Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes. | False | number | None | None | None | |
| NGS RNA RIN | A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number | False | number | None | None | None | |
| NGS RNA DV200 | Represents the percentage of RNA fragments that are >200 nucleotides in size. Number | False | number | None | None | None |