Human Ovarian Cancer: Targeted-Compare, Immunology Panel. Stains: DAPI, Anti-PanCK, Anti-CD45
Spatial Gene Expression dataset analyzed using Space Ranger 1.2.0
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10X Genomics obtained fresh frozen Endometrial Adenocarcinoma of the ovary tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide Demonstrated Protocol (CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained with antibodies and DAPI following Methanol Fixation, Immunofluorescence and Staining Protocols (CG000312).
Samples were stained with antibodies and DAPI as follows:
- 1:150 dilution of Alexa Fluor 488 anti-Cytokeratin (pan reactive) Antibody (P/N 628608, BioLegend)
- 1:100 dilution of Alexa Fluor 647 anti-human CD45 Antibody (P/N 304020, BioLegend)
- DAPI
The cloupe and TIFF files available for download here contain multiple channels or pages respectively. The following table describes the filters and stains corresponding to the channels/pages.
| Channel | Filter | Stain |
|---|---|---|
| 1 | DAPI | DAPI |
| 2 | FITC | Cytokeratin (pan reactive) |
| 3 | TRITC | Fiducial Frame |
| 4 | Cy5 | CD45 |
Visium whole transcriptome gene expression libraries (T1T2-H6) were prepared as described in the Visium Spatial Reagent Kits User Guide (CG000239 Rev D) and sequenced on a NovaSeq 6000.
Targeted libraries were prepared following the Targeted Gene Expression - Spatial User Guide (CG000377) using the Human Immunology Panel (PN-2000286) and sequenced on a NovaSeq 6000.
The targeted-compare pipeline in Space Ranger was used to compare the parent whole transcriptome analysis (WTA) with the immunology targeted analysis. While it is not necessary to compare the WTA and targeted data when doing targeted gene expression, if both the targeted and parent samples have been sequenced, the targeted-compare pipeline may be used to compare the two samples.
Key metrics were:
- Mean Reads per Tissue-Covered Spot: 10,390 (targeted); 80,586(WTA)
- Median Targeted Genes per Tissue-Covered Spot: 211 (targeted); 196 (WTA)
- Median Targeted UMIs per Tissue-Covered Spot: 456 (targeted); 501 (WTA)
- Mean UMI recovery ratio (targeted vs. parent): 1.209
- Pearson correlation of log10 UMI counts per gene: 0.987
To maintain donor anonymity, sequence data for this sample is not currently available.
This dataset is licensed under the Creative Commons Attribution license.