Question: Are Microbeads (Miltenyi Biotec) and EasySep beads (STEMCELL) compatible with the 10x Single Cell RNA-seq workflow?
Answer: Miltenyi Biotec Microbeads are fully compatible with the Chromium Controller and Single Cell 3' Gene Expression and Single Cell Immune Profiling solutions, both for positive and negative selection of cells. The beads are small enough that they do not interfere with partitioning or emulsion stability. We have several Demonstrated Protocols using Microbeads with the 10x system:
- Enrichment of CD3+ T cells from dissociated tissue
- Removal of dead cells from single-cell suspensions
- Also refer to page 24 of our Cell Preparation Guide
We have also successfully used other magnetic beads, such as EasySep from STEMCELL Technologies and Dynabeads from Invitrogen, for negative selection of T or B cells for our Barcode Enabled Antigen Mapping (BEAM) assay. See:
These beads are likely to also be successful for other applications with 10x Genomics Single Cell Gene Expression and Single Cell Immune Profiling assays. However, we have not specifically tested these beads for positive selection upstream of 10x assays (only negative selection was tested with the BEAM assay).
Please see the following resources and customer publication for EasySep beads:
Please note that some buffers used during bead enrichment protocols may contain EDTA. We recommend that the final concentration of EDTA in the cell suspension is less than 0.1 mM EDTA, as EDTA is an inhibitor of reverse transcription. If using a buffer that contains EDTA, make sure to thoroughly wash the suspension to remove as much as possible before loading the sample into the chip.
Products: Single Cell Gene Expression, Single Cell Immune Profiling