Top 5 Questions on Our Flexible Single-cell RNA-seq Solution

Mary BowenArticle

1. Can I increase the cell concentration?
Increasing the cell concentration will increase the probability of having two or more cells in a drop. To avoid doublets, we recommend a cell concentration between 80,000 and 100,000 cells/ml. If your application does not require 1 cell per droplet, increasing the cell concentration will decrease encapsulation time. Doublets can often be detected in bioinformatic analysis after sequencing and removed from the data set.

2. What are my best options for sequencing platform?

Illumina’s NextSeq is the best platform for single-cell analysis. NovaSeq can also be used, but there are some precautions you should take to avoid “index-hopping” and proper index sequencing.

3. My sample was sequenced on an Illumina NovaSeq system and I had a lot of mis-assigned sample reads!

You may have experienced “index-hopping”. Ilumina has some recommendations about how to avoid this. Also, read this journal article about a novel way to avoid this problem:

https://www.biorxiv.org/content/10.1101/835488v1 (to be published in the next issue of BMC Genomics)

4. What does 1CellBio recommend for analyzing my data after my samples have been sequenced?

The best option for most of our customers is to take advantage of the free trial of the software package offered by Partek® Flow®.

5. What is the platforms running cost on a per sample basis?

Since our platform is open, the customer has control over experimental setup and how they want to design the experiment. Our typical running costs are $0.06 per cell with the flexibility to decrease the cost even further.