The Single Cell Fixed RNA Profiling (FRP) workflow measures RNA levels in samples (single cells or nuclei) fixed with formaldehyde, using probes targeting the whole transcriptome. After whole transcriptome probe panels are added to the sample, each probe pair hybridizes to its target gene and is then ligated.

After June 30, 2023, new Cell Ranger releases will no longer support Targeted Gene Expression analysis. Targeted Gene Expression technology focuses on a selected panel of relevant targeted genes which are directly enriched from a Chromium single cell gene expression library prior to …

10x Genomics Chromium Single Cell Gene Expression. Cell Ranger7.1 (latest), printed on 07/28/2023. Gene Expression Metrics. Cell Ranger pipelines output key metrics in text format. Below are the definitions of the reported metrics. cellranger count/multi metrics definitions; Targeted Gene Expression metrics definitions; cellranger aggr metrics ...

Cell calling for Targeted Gene Expression. Cell Ranger includes dedicated cell calling algorithm (introduced in 4.0) that is applied specifically to identify cells from Targeted Gene Expression datasets.

The pipeline outputs a unified feature-barcode matrix that contains gene expression counts alongside Feature Barcode counts for each cell barcode. The feature-barcode matrix replaces the gene-barcode matrix emitted by older versions of Cell Ranger.

In the example below we describe how to construct an MRO file to specify multiple libraries as well as multiple flow cells (since most often the multiple libraries will have been sequenced on different runs).

10x Genomics Single Cell CNV. Cell Ranger DNA , printed on 02/09/2025.

10x Genomics Single Cell ATAC. Cell Ranger ATAC , printed on 02/13/2025.

10x Genomics Single Cell Gene Expression. Cell Ranger , printed on 01/28/2025.

After June 30, 2023, new Cell Ranger releases will no longer support Targeted Gene Expression analysis. Overview Targeted Gene Expression technology uses selected panels of relevant targeted genes.