Visium RNA Level 1
Attribute: Visium Capture Area¶
| Valid Value | Description | Ontology |
|---|---|---|
| A | Capture area A, one of four positions (A, B, C, D) on this 10x Genomics Visium slide format; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| B | Capture area B, one of four positions (A, B, C, D) on this 10x Genomics Visium slide format; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| C | Capture area C, one of four positions (A, B, C, D) on this 10x Genomics Visium slide format; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| D | Capture area D, one of four positions (A, B, C, D) on this 10x Genomics Visium slide format; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| A1 | Capture area A1, one of the four standard positions (A1, B1, C1, D1) on a 10x Genomics Visium slide; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| B1 | Capture area B1, one of the four standard positions (A1, B1, C1, D1) on a 10x Genomics Visium slide; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| C1 | Capture area C1, one of the four standard positions (A1, B1, C1, D1) on a 10x Genomics Visium slide; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
| D1 | Capture area D1, one of the four standard positions (A1, B1, C1, D1) on a 10x Genomics Visium slide; each capture area contains a grid of spatially barcoded spots used to capture mRNA from a mounted tissue section. | Not available |
Attribute: Visium Slide Version¶
| Valid Value | Description | Ontology |
|---|---|---|
| V1 | 10x Genomics Visium Spatial Gene Expression slide, version 1 (the original, manually placed Visium slide format), with capture areas measuring 6.5mm x 6.5mm containing 4,992 spatially barcoded spots each. | EFO:0022857 |
| V2 | 10x Genomics Visium slide, version 2, compatible with the Visium CytAssist instrument for automated tissue transfer from a standard glass slide; available with capture areas of 6.5mm x 6.5mm or 11mm x 11mm. | EFO:0022858 |
| V3 | A later generation of the 10x Genomics Visium slide, succeeding versions 1 and 2 in this model's slide-version series. 10x Genomics has not published a distinct 'V3' Visium slide specification in public ontology sources, so exact design differences from earlier versions are not documented here. | Not available |
| V4 | The most recent generation of the 10x Genomics Visium slide referenced in this model, succeeding versions 1 through 3. 10x Genomics has not published a distinct 'V4' Visium slide specification in public ontology sources, so exact design differences from earlier versions are not documented here. | Not available |
Attribute: Visium Image Re-orientation¶
| Valid Value | Description | Ontology |
|---|---|---|
| True | Conforming to facts, reality, or definitive criteria. | NCIT:C68850 |
| False | Not in accordance with facts, reality, or definitive criteria. | NCIT:C68851 |
Attribute: Visium Spatial Read1¶
| Valid Value | Description | Ontology |
|---|---|---|
| cDNA | Single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase. | NCIT:C324 |
| Spatial Barcode and UMI | A sequencing read that contains the spatial barcode and unique molecular identifier (UMI) sequences used to assign reads to their spatial location and de-duplicate transcript counts. | Not available |
Attribute: Visium Spatial Read2¶
| Valid Value | Description | Ontology |
|---|---|---|
| cDNA | Single-stranded DNA that is complementary to messenger RNA or DNA that has been synthesized from messenger RNA by reverse transcriptase. | NCIT:C324 |
| Spatial Barcode and UMI | A sequencing read that contains the spatial barcode and unique molecular identifier (UMI) sequences used to assign reads to their spatial location and de-duplicate transcript counts. | Not available |
Attribute: Visium Spatial Library Construction Method¶
| Valid Value | Description | Ontology |
|---|---|---|
| Smart-seq2 | Switching mechanism at the 5' end of RNA templates (SMART)-based library construction method; Smart-seq2 transcriptome libraries have improved detection, coverage, and accuracy compared to the original Smart-seq method, and are generated with off-the-shelf reagents at lower cost. | EFO:0008931 |
| Smart-SeqV4 | Single-cell RNA-seq library construction method using SMART (Switching Mechanism At 5' end of RNA Template) chemistry to generate high-quality cDNA from ultra-low amounts of total RNA or directly from intact cells (<1,000 cells); improves on Smart-seq2 via locked nucleic acid (LNA) technology and an optimized template-switching oligo. | EFO:0700016 |
| 10xV1.0 | First version (v1) of the 10x Genomics droplet-based single-cell 3' library construction chemistry, in which barcoded gel beads and cells are co-encapsulated in nanoliter droplets for parallel barcoding of transcripts. | EFO:0009901 |
| 10xV1.1 | Minor revision (v1.1) of the first-generation 10x Genomics single-cell 3' library construction chemistry; specific chemistry differences from v1.0 are not documented in public ontology sources. | Not available |
| 10xV2 | Second version (v2) of the 10x Genomics droplet-based single-cell 3' library construction chemistry, in which the poly(dT) sequence is part of the gel bead oligo (along with the cell barcode and UMI) and the template-switch oligo is supplied in the RT primer. | EFO:0009899 |
| 10xV3 | Third version (v3) of the 10x Genomics droplet-based single-cell 3' library construction chemistry. | EFO:0009922 |
| 10xV3.1 | Minor revision (v3.1) of the third-generation 10x Genomics single-cell 3' library construction chemistry. | EFO:0022980 |
| Drop-seq | Droplet microfluidics-based method for parallel analysis of mRNA transcripts from thousands of individual cells, in which each cell is co-encapsulated with a barcoded bead in a nanoliter droplet. | EFO:0008722 |
| inDropsV2 | Second version (v2) of the inDrop (indexing droplets) single-cell RNA-seq library construction method, a droplet microfluidic platform that uses hydrogel beads to deliver barcoded primers to individual cells. | Not available |
| inDropsV3 | Third version (v3) of the inDrop (indexing droplets) single-cell RNA-seq library construction method. | Not available |
| TruDrop | Droplet-based microfluidic single-cell library construction platform based on inDrop that incorporates dual indexing to detect index hopping, using standard Illumina sequencing primers for high-throughput sequencing. | EFO:0700010 |
| Nextera XT | Illumina library preparation kit that uses tagmentation (simultaneous enzymatic fragmentation and adapter tagging) to construct sequencing-ready libraries from very low quantities of input DNA/cDNA; commonly used as a downstream library-prep step following methods such as Smart-seq2. | Not available |