10X Genomics Chromium X Controller
The 10X Genomics Chromium X is used to generate thousands of Gel bead-in-emulsion (GEMs) droplets, enabling partitioning and barcoding of single cells or nuclei, in micro reactions. The Chromium X is the new version of their Chromium controller, enabling running the 10X high throughput kits with up to 16 samples per chip and a total of 320.000 recovered cells, without multiplexing, and 960.000 recovered cells with multiplexing per chip. In addition the Chromium X also adds support for the 10X Gene Expression Flex kit, enabling scRNASeq analysis of PFA fixed cells/nuclei or cells recovered from FFPE treated tissue samples.
Single cell RNAseq specifications
| Cells recovered/sample | 500-20000 (Up to 60K with multiplexing) |
|---|---|
| Number of Samples/run | 1-16 (Up to 192 with multiplexing) |
| Run time | 18 min. |
| Read pairs/cell (3´v3.1) | Min. 20.000 |
| Cell Size | Max. 30 µm |
| Cell viability | ≥90% |
| Cell capture rate | Max. 65% |
| Illumina Seq kits | Min. 2 x 50 bp (NovaSeq) |
Most high quality single cell suspensions (max. cell size 30 µm) should be compatible. It is possible to test a given cell line on the chromium controller using a training kit.
How many cells (scRNASeq)
The number of cells per sample is highly dependent on the number of cell types present in the sample and the fractional abundances of the rarest cell types. If you have an idea about the heterogeneity of the sample, you can use the calculator developed by the SATIJA LAB to estimate a minimum number of cells/sample.
Link to calculator: https://satijalab.org/howmanycells
Sequencing depth (scRNASeq)
10X recommends a minimum sequencing depth of 20.000 Read pairs/cell (scRNASeq 3´v3.1). However, as with the number of cells, the number of read pairs/cell depends on several factors like biological question asked, mRNA content of the cells, transcriptional heterogeneity etc. More info in the links below.
Schematic guideline of the Novaseq flowcell to use at a given cell number and sequencing depth.
Information on sequencing depth/sequencing saturation:
https://kb.10xgenomics.com/hc/en-us/articles/115005062366-What-is-sequencing-saturation-
Other Applications
Single cell Gene Expression Analysis
Reveal the Full Complexity of Cellular Diversity, Cell by Cell.
Single Cell Immune Profiling
Combine Single cell VDJ sequencing, antigen specificity and Gene expression analysis.
Single cell ATAC sequencing and Gene expression analysis
Analyze the chromatin accessibility on a single cell level with or without Gene Expression analysis.
Single cell Gene Expression Analysis from PFA Fixed Cells/Nuclei or FFPE Tissue
Add extra flexibility to your studies by PFA fixating cells or nuclei before Gene Expression analysis.