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I heard the term Feature Barcoding a lot so I find resources to understand it. I have read docs of 10xgenomics and I see that Feature Barcoding technology is a method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays, this technology also do something with t-SNE and something with matrices.

I can't imagine the whole picture because I don't know what are those adding extra channels of information to cells, single-cell gene expression and parallel with other assays mean. And what is the input and output of this technology? Is there any paper go along with this technology?

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  • $\begingroup$ Welcome to the site. Have you looked at the 10X genomics website? Usually they post all the papers and materials. How you done pubmed or google scholar search for papers? $\endgroup$ – Bioathlete Feb 10 '19 at 3:40
  • $\begingroup$ I did but I only found this paper relates to the term "Feature Barcoding" when some people tweeted about https://www.biorxiv.org/content/10.1101/237693v1 , and this paper in Feature Barcoding Glossary https://www.nature.com/articles/nmeth.4380 . But I cannot find the whole match "Feature Barcoding" in that paper which make me unclear how it relates to each other. $\endgroup$ – Trong-Thang Pham Feb 10 '19 at 14:18
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"Feature Barcoding" refers to using antibodies linked to specific oligos. The antibodies can then bind to cell surface markers of interest and the oligos they're conjugated with turned into normal scRNA-seq reads. This effectively means you can get a FACs profile for each cell without needing to run it through a FACs sorter and individually label it.

The "feature barcoding" nomenclature comes from 10X I think, but there are a few similar protocols (maybe they're exactly the same in the end, I'm not sure about the details) such as CITE-seq and REAP-seq. You can see a talk from 10X on this here.

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  • $\begingroup$ Thank you so much. Now it's more clear for me. May you suggest any paper come with it? I found some paper but don't know which one is better for understanding: https://www.nature.com/articles/nmeth.4380 or https://www.biorxiv.org/content/10.1101/237693v1 $\endgroup$ – Trong-Thang Pham Feb 10 '19 at 14:10
  • $\begingroup$ I've updated my answer, the nature methods paper you linked to at least is related (I mentioned it in my update). The cell hashing paper you mentioned is also very related. $\endgroup$ – Devon Ryan Feb 10 '19 at 19:53
  • $\begingroup$ Thanks. I think this is it. I didn't know there is a talk about it. Thank you again for your answer. I will dig into it. $\endgroup$ – Trong-Thang Pham Feb 11 '19 at 2:03

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