Question: Can I pool leftover gel beads from multiple wells to run additional samples?
Answer: No. We do not recommend pooling leftover gel beads because of 10x barcode overlap and contamination risk. There are roughly 750,000 gel beads per well, and each gel bead contains oligos with a unique 10x barcode. Each well contains the same 750,000 gel beads with the same 10x barcodes. We do not recommend pooling gel beads across wells because the chance of two cells being partitioned with a gel bead containing the same barcode is increased.
In addition to barcode overlap, increased handling of the gel beads may alter the ratio of gel beads in solution, affecting the partitioning of gel beads into GEMs, and can introduce particulates or debris that may clog the chip and lead to a failed run. The gel bead wells are designed as single use to reduce these risks.