Mixture of Colorectal Cancer and Healthy Kidney FFPE Tissues Dissociated Manually or using gentleMACS Dissociator, Multiplexed Samples, 4 Probe Barcodes (Next GEM)

This dataset is paired to these Visium CytAssist Spatial Gene Expression for FFPE datasets, where the same FFPE block was used for both assays:

• Human Colorectal Cancer, 11 mm Capture Area (FFPE)
• Human Kidney, 11 mm Capture Area (FFPE)

Formalin-fixed paraffin-embedded (FFPE) specimens from two different human tissues were obtained by 10x Genomics from Discovery Life Sciences and Avaden Biosciences:

• Colorectal Cancer, Adenocarcinoma (Male, Age mid 60s, FFPE Block Age 2 years, DV200: 67)
• Healthy Kidney (Female, Age mid 60s, FFPE Block Age 3 years, DV200: 42)

Cells were isolated from two, 25 micron sections following the demonstrated protocol Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling (CG000632), using both the gentleMACS Octo Dissociator and Manual Dissociation options for each tissue.

The Fixed RNA Gene Expression library was generated as described in the Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527, Rev C). Samples were run as a 4-sample multiplexed experiment, in which each sample was hybridized with a unique Probe Barcode in a separate hybridization reaction. After hybridization, samples were pooled in equal proportions, washed, and then run in a single GEM lane. The resulting library was sequenced on an Illumina NovaSeq6000 with approximately 20k read pairs per cell.

• Total 41,127 cells detected (Colorectal Cancer, Manual: 9,447; Colorectal Cancer, Octo Dissociator: 13,284; Kidney, Manual: 8,023; Kidney, Octo Dissociator: 10,373)
• Paired-end, dual indexing: 28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2

Brightfield and propidium iodide fluorescence images of the resulting cell suspensions after dissociation are provided, as well as images of the final pooled sample (also shown below).

Brightfield	Fluorescence

This dataset is licensed under the Creative Commons Attribution license.