Human Colorectal Cancer: Whole Transcriptome Analysis
Spatial Gene Expression dataset analyzed using Space Ranger 1.2.0
![](https://cdn.10xgenomics.com/image/upload/v1724182202/datasets/detail/datasets_visium.png)
Learn about Visium analysis
10X Genomics obtained fresh frozen Invasive Adenocarcinoma of the large intestine 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 following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).
The tissue was AJCC/UICC T4aN0M0, Stage Group IIB.
The H&E image was acquired using a Nikon Eclipse Ti2-E microscope with the following settings:
- Color camera
- 10X objective
- Numerical Aperture: 0.45
- Exposure: 20 ms
The Visium Gene Expression library (T1T2-E8) was prepared as described in the Visium Spatial Reagent Kits User Guide (CG000239 Rev D). Sequencing data was processed using Space Ranger.
- Sequencing instrument: Illumina NovaSeq 6000, flow cell HHYWHDSXY (lanes 1-4)
- Sequencing depth: 112,228 mean reads per cell
- Sequencing configuration: Paired-end (28 X 90), Dual-Indexed Sequencing. Read 1: 28 cycles (16 bp barcode, 12 bp UMI); i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles (transcript).
- Slide: V10A13-206
- Area: C1
Key metrics were:
- Spots detected: 3,138
- Median genes per spot: 3,538
- Median UMI counts per spot: 8,906
To maintain donor anonymity, sequence data for this sample is not currently available.
This dataset is licensed under the Creative Commons Attribution license.