Aggregate of Human PBMCs Comparing Next GEM Fixed RNA Profiling vs GEM-X Flex Gene Expression

Peripheral blood mononuclear cells (PBMCs) were obtained from AllCells by 10x Genomics. A total of 5 million cells were thawed following the demonstrated protocol for Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (CG000478). After thawing, the cells were split into two samples and fixed for 1 hour at room temperature, using either the protocol for Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling (CG000478) or the Fixation of Cells & Nuclei for GEM-X Flex Gene Expression (CG000782).

Next GEM Fixed RNA Profiling Gene Expression libraries for Flex were generated as described in the Chromium Fixed RNA Profiling for Singleplexed Samples (CG000477), and Gene Expression libraries for GEM-X Flex were generated as described in the GEM-X Flex Gene Expression Reagent Kit for Singleplex samples (CG000786). Gene expression libraries were sequenced on an Illumina NovaSeq 6000 to a read depth of approximately 20,000 mean reads per cell using a paired-end, dual indexing sequencing scheme:

• 28 cycles Read 1
• 10 cycles i7
• 10 cycles i5
• 90 cycles Read 2

Libraries were analyzed using the cellranger multi pipeline. The outputs of each sample were then aggregated and normalized to equal sequencing depth using the cellranger aggr pipeline, generating a single set of output files containing data from all individual samples.

The sample-level web summaries from cellranger multi runs are available for download here.

This dataset is licensed under the Creative Commons Attribution license.