<p>I believe it is mostly a cost issue as spike-ins are "expensive" to use given the large number of cells that are/can be sequenced via droplet based methods (as compared to plate-based ones). The 10x link that you provided actually states that this is possible with 10x and Klein et al. used ERCC spike-ins in 953 droplets (Cell. 2015 May 21;161(5):1187-1201. doi: 10.1016/j.cell.2015.04.044.). </p>

CC BY-SA 4.0
2018-11-12T11:11:19.027Z
2018-11-12T11:11:19.027Z
haci
<p>By reading Bacher &amp; Kendziorski (2016), I found the following statement:</p>

<blockquote>
  <p>recent droplet technologies are not yet able to accommodate spike-ins</p>
</blockquote>

<p>What's the reason why current droplet technologies cannot use spike-ins? By searching through the available methodologies I found <a href="https://community.10xgenomics.com/t5/Single-Cell-Forum/Thoughts-on-ERCC-Spike-Ins/td-p/207" rel="nofollow noreferrer">this question</a> on 10X community, but still I cannot understand what is the problem created by using spike-ins with droplet technologies.</p>

<ol>
<li>Bacher, R. &amp; Kendziorski, C. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823857/" rel="nofollow noreferrer">Design and computational analysis of single-cell RNA-sequencing experiments</a>. Genome Biol. 17, 63 (2016).</li>
</ol>

<scrnaseq><spike-in>
Is it possible to use spike-ins with droplet technologies?
# Is it possible to use spike-ins with droplet technologies?

(Asked by: username_0 on 2018-04-05)

By reading Bacher & Kendziorski (2016), I found the following statement:

> recent droplet technologies are not yet able to accommodate spike-ins

What's the reason why current droplet technologies cannot use spike-ins? By searching through the available methodologies I found [this question](https://community.10xgenomics.com/t5/Single-Cell-Forum/Thoughts-on-ERCC-Spike-Ins/td-p/207) on 10X community, but still I cannot understand what is the problem created by using spike-ins with droplet technologies.

1. Bacher, R. & Kendziorski, C. [Design and computational analysis of single-cell RNA-sequencing experiments](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4823857/). Genome Biol. 17, 63 (2016).

**Tags:** scrnaseq, spike-in

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## 1 answers

### Answer by username_1 on 2018-11-12. Score: 1

I believe it is mostly a cost issue as spike-ins are "expensive" to use given the large number of cells that are/can be sequenced via droplet based methods (as compared to plate-based ones). The 10x link that you provided actually states that this is possible with 10x and Klein et al. used ERCC spike-ins in 953 droplets (Cell. 2015 May 21;161(5):1187-1201. doi: 10.1016/j.cell.2015.04.044.).


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