<p>From <a href="https://www.genome.gov/26524238/encode-project-common-cell-types/" rel="nofollow noreferrer">Encode's website</a>:</p>

<blockquote>
  <p>... To aid in the integration and
  comparison of data produced using different technologies and
  platforms, the ENCODE Consortium has designated cell types that will
  be used by all investigators. These common cell types include both
  cell lines and primary cell types, and plans are being made to explore
  the use of primary tissues and embryonic stem (ES) cells.</p>
  
  <p>Cell types were selected largely for practical reasons, including
  their wide availability, the ability to grow them easily, and their
  capacity to produce sufficient numbers of cells for use in all
  technologies being used by ENCODE investigators. Secondary
  considerations were the diversity in tissue source of the cells, germ
  layer lineage representation, the availability of existing data
  generated using the cell type, and coordination with other ongoing
  projects. Effort was also made to select at least some cell types that
  have a relatively normal karyotype...</p>
</blockquote>

CC BY-SA 3.0
2017-05-26T20:27:47.253Z
2017-05-26T20:27:47.253Z
emilliman5
<p>The tiers denote the original priority of sequencing and processing the samples. This is understandable given the number of marks and experiment types that ENCODE tried to sequence. Further details are available on <a href="http://genome.ucsc.edu/ENCODE/cellTypes.html" rel="noreferrer">ENCODE's website</a>. </p>

<p><strong>Edit</strong>: Just to expand a bit, tier one cells were supposed to get processed first. Then tier 2 came second. Of course tier 2 had a LOT more cells, so it got split into 2 and 2.5, since there were already apparently tier 3 cells.</p>

CC BY-SA 3.0
2017-05-25T18:44:04.180Z
2017-05-25T18:44:04.180Z
Devon Ryan
<p><a href="https://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixHuman.html" rel="noreferrer">The ENCODE Experiment Matrix at UCSC</a> lists the different available cell types under the categories "Tier 1", "Tier 2" and "Tier 3". What is the difference between these classifications?</p>

<p>What, for example, makes GM12878 a Tier 1 cell type and A549 a Tier 2 cell type?</p>

<p><a href="https://i.sstatic.net/Ejhqx.png" rel="noreferrer"><img src="https://i.sstatic.net/Ejhqx.png" alt="enter image description here"></a></p>

CC BY-SA 3.0
2017-05-25T19:44:09.777Z
You should read [A User's Guide to the Encyclopedia of DNA Elements (ENCODE)](http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046)
Chris_Rands
<encode>
What is the difference between ENCODE Tier 1, 2 and 3 cell types?
# What is the difference between ENCODE Tier 1, 2 and 3 cell types?

(Asked by: username_0 on 2017-05-25)

[The ENCODE Experiment Matrix at UCSC](https://genome.ucsc.edu/ENCODE/dataMatrix/encodeDataMatrixHuman.html) lists the different available cell types under the categories "Tier 1", "Tier 2" and "Tier 3". What is the difference between these classifications?

What, for example, makes GM12878 a Tier 1 cell type and A549 a Tier 2 cell type?

[![enter image description here](https://i.sstatic.net/Ejhqx.png)](https://i.sstatic.net/Ejhqx.png)

**Tags:** encode
> **Comments:**
> **username_1**: You should read [A User's Guide to the Encyclopedia of DNA Elements (ENCODE)](http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001046)  

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## 2 answers

### Answer by username_3 on 2017-05-25. Score: 6 | Accepted answer

The tiers denote the original priority of sequencing and processing the samples. This is understandable given the number of marks and experiment types that ENCODE tried to sequence. Further details are available on [ENCODE's website](http://genome.ucsc.edu/ENCODE/cellTypes.html).

**Edit**: Just to expand a bit, tier one cells were supposed to get processed first. Then tier 2 came second. Of course tier 2 had a LOT more cells, so it got split into 2 and 2.5, since there were already apparently tier 3 cells.


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### Answer by username_2 on 2017-05-26. Score: 1

From [Encode's website](https://www.genome.gov/26524238/encode-project-common-cell-types/):

> ... To aid in the integration and
> comparison of data produced using different technologies and
> platforms, the ENCODE Consortium has designated cell types that will
> be used by all investigators. These common cell types include both
> cell lines and primary cell types, and plans are being made to explore
> the use of primary tissues and embryonic stem (ES) cells.
>
> Cell types were selected largely for practical reasons, including
> their wide availability, the ability to grow them easily, and their
> capacity to produce sufficient numbers of cells for use in all
> technologies being used by ENCODE investigators. Secondary
> considerations were the diversity in tissue source of the cells, germ
> layer lineage representation, the availability of existing data
> generated using the cell type, and coordination with other ongoing
> projects. Effort was also made to select at least some cell types that
> have a relatively normal karyotype...


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