Human Lung Cancer, 11 mm Capture Area (FFPE)
Spatial Gene Expression dataset analyzed using Space Ranger 2.0.1
![](https://cdn.10xgenomics.com/image/upload/v1724182202/datasets/detail/datasets_visium.png)
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10x Genomics obtained FFPE human lung cancer tissue from Avaden Biosciences. The tissue was sectioned as described in the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide (CG000518). Tissue section of 5 µm was placed on a standard glass slide, then stained following the Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression Slide v2, with 11 mm capture areas following the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495).
- Diagnosis: Lung Cancer, Neuroendocrine Carcinoma
- Stage (AJCC): IB
- TNM system: T2aN0MX
- FFPE Block Age < 1 year
- DV200: 73
The H&E image was acquired using Olympus VS200 Slide Scanning Microscope with these settings:
- Olympus Objective magnification: 20x UPLXAPO Objective
- Numerical Aperture: 0.8
- ScopeLED light source: Xcite Novum
- Camera: VS-264C
- Exposure: 500 µs
From the H&E image, vascular invasion and some compressed hemorrhage portion in the tumor, along with a clear stromal boundary outside the solid tumor region can be observed.
Libraries were prepared following the Visium CytAssist Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000495).
- Sequencing instrument: Illumina NovaSeq 6000, flow cells HJWFGDSX5 and HJW2WDSX5 (lane 1-4)
- Sequencing depth: 844,866,053 reads / 45.9% saturation
- Sequencing configuration: 28bp read 1 (16bp Visium spatial barcode, 12bp UMI), 90bp read 2 (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
- Dual-Index set: SI-TS-B3
- Slide: V52Y10-286
- Area: B1
Key cell metrics were:
- Spots detected under tissue: 6,195
- Median UMI counts per spot: 66,268
- Median genes per spot: 10,087
This dataset is licensed under the Creative Commons Attribution license.