Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling

Overview

This dataset is associated with the preprint titled Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling. See the preprint for full details on methods and results.

Tissue sectioning

5 µm sections were taken from the FFPE tissue blocks with a microtome (Epredia HM355S). Sections were adjacent or near-adjacent (within 5-10 µm of each other). Sectioning followed the Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide (CG000518, Rev C).

Library preparation & sequencing

We placed FFPE tissue sections on plain glass slides for deparaffinization, H&E staining and imaging following the Visium HD FFPE Tissue Preparation Handbook (CG000684). Probe hybridization, probe ligation, slide preparation, probe release, extension, library construction, and sequencing followed the Visium HD Spatial Gene Expression Reagent Kits User Guide (CG000685). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end reads (43 cycles Read 1, 10 cycles i7, 10 cycles i5, 50 cycles Read 2).

Analysis

Space Ranger v3.0 (10x Genomics) was used to map FASTQ files to the human reference, detect the tissue section, align the sequencing data to the microscope image and the CytAssist image, and output gene-barcode matrices for further analysis.

Note that to process the FASTQ and image files using spaceranger count, the slide layout file must be downloaded and the --slidefile option must be used.

How to view data

Interactively explore the Loupe Browser file (.cloupe) with Loupe Browser v8.0 or later. For details on the other outputs, see the Space Ranger Outputs Overview.