Aggregate of Human Renal Cell Carcinoma Cells at Various Storage Timepoints

Cells from a dissociated Renal Cell Carcinoma tumor (Kidney Cancer, Female, Age mid 60s) were obtained by 10x Genomics from Discovery Life Sciences and fixed for 24h at 4°C following the demonstrated protocol Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (CG000478). Following fixation, cells were divided and used immediately to generate Fixed RNA Gene Expression libraries (day 0), or stored under various conditions (short-term storage after fixation for 3 days or 7 days at 4°C; long-term storage for 1 month at -80°C) before being used to generate Gene Expression libraries.

Fixed RNA Gene Expression libraries were generated as described in the Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527) using the Chromium X. Samples from a given timepoint were run as a 4-sample multiplexed experiment, in which the kidney cancer cells were hybridized with BC004, and the other Probe Barcodes were hybridized with cells from three other dissociated tumor samples (not described here). After hybridization, samples were pooled in equal proportions, washed, and then run in a single GEM lane.

For cells that were used to immediately generate Gene Expression libraries, the sample remaining after GEM generation was then stored for 1 month at -80°C, and subsequently used to generate a second set of Gene Expression libraries (long-term storage for 1 month post-hybridization at -80°C).

The resulting libraries were sequenced on an Illumina NovaSeq6000 and analyzed with the cellranger multi pipeline. The outputs from only the kidney cancer samples at various timepoints were then aggregated and normalized to equal sequencing depth (~37k read pairs per cell) using the cellranger aggr pipeline to generate a single set of output files containing all of the data from each of the individual samples.

Storage conditions:

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This dataset is licensed under the Creative Commons Attribution license.