Question: What are the Gel bead color codes in OCM and how do they relate to the OCM barcode lists? Do the color and order matter in workflow and analysis?
Answer:
The gel bead color codes for the four OCM barcode lists are consistent between 3' and 5' OCM; however, the order in which the colors appear differs between the two.
For 3' OCM, the gel-bead color and barcode lists are as follows:
- Blue gel beads = OB1
- Red = OB2
- Yellow = OB3
- Green = OB4
Below is an workflow image of a 3' OCM experiment with samples labeled in order. The numbers 1, 2, 3, and 4 correspond to OB1, OB2, OB3, and OB4, respectively.
For 5'OCM, the color order is Blue, Red, Green, Yellow with the corresponding barcode lists as follows:
- Blue = OB1
- Red = OB2
- Green = OB3
- Yellow = OB4
NOTE: From an analysis perspective, the order of the samples isn't crucial, and Cell Ranger doesn't require a specific order. What’s important is that the correct OCM barcode IDs are provided for each sample to ensure accurate demultiplexing. To avoid issues, consider the following recommendations:
- Verification: Always verify that the barcode lists in your experimental documentation match those used in your analysis pipelines.
- Documentation Consistency: Maintaining consistent documentation across your experiments and analysis files will help prevent errors and ensure reproducibility.
Related Article: GEM-X Universal Multiplex (OCM) Barcode lists and understanding its usage
Products: Single Cell 3' Universal Multiplex, Single Cell 5' Universal Multiplex
Last Updated: Mar 20, 2025