10x Genomics GSF Recommendations

1.  Requiring a full consultation before anything is started- It’s critical that the end-customer fully understands how many cells \samples they ultimately want to run and how much sequencing they intend to do.

  • Reviewing sequence saturation concept and make sure users understand that they may need additional sequencing power if they need to detect every single possible transcript
  • Review that the key to the assay is intact, viable cells
  • Recommend dry runs where they perfect their cell prep methodology
  • Never have the first experiment with a new cell type be with a scarce or precious sample,
  • Review that if viability looks poor on the day of their experiment, they should try their prep again

2. Setting a hard cutoff for submission time-   From the time the cells come through GSF’s door and the GSF team members will do the QC and get the emulsions into the thermocycler will take at least an hour, and likely 2 hours if there are many samples. The GSF team members will have to prepare all reagents before the cell submission. Stick on your timeline and inform the GSF if you can’t make the timeline immediately.

3. Setting clear submission criteria- cells must be provided at their final intended concentration and buffer.  So with abundant cells, they would be targeting 1,000 cells/ul and be in the PBS+BSA.

4. Setting “cutoffs” for viability- The GSF requests to have our users essentially to be present in the step of sample QC so we can make a decision together if something is not optimal. Users will sign a liability waiver if they want to run cells with very low viability (< 80%).  It is critical for users to understand that the QC during the assay will not reveal how much of impact viability had, and they will have to sequence their libraries and only then find that their data may be impacted.