NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

Cell types

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ENCODE Common Cell Types (Tier 1)

The ENCODE Consortium has identified common cell types that will be studied by all investigators to aid in the integration and comparison of data produced using different technologies and platforms. Tier 1 cells are of higher priority and should be analyzed sooner than Tier 2 cells if possible.


ENCODE Common Cell Types (Tier 2)


Criteria for selection of ENCODE Tier1/Tier2 cell types

A summary of the selection criteria is here. The full document describing the rationale for selection is here.

Measurements for the ENCODE common cell types

To ensure consistency in cell cultures prepared in different laboratories, investigators should take certain measurements for each cell harvest. A list of these measurements is available here.

Cell phenotype study

Gene expression studies for ENCODE cell preps, provided by the Tenenbaum lab at SUNY-Albany

Recent Requests for Tier 2.5 Cells

4 May 2012 Tier 2.5 Requests

ENCODE Additional Cell Types (Tier3)

Tier 3 cell types are additional types selected for use by individual ENCODE investigators once analyses of the Tier 1 and Tier 2 cells have been completed. All Tier 3 cell types used must be registered with the DCC before data can be submitted for experiments using that cell type. Before registration, a cell culture protocol for the cell type must be approved by the Common Resources Working Group.

To begin the registration process for a new Tier 3 cell type: enter the information for that cell type into the table below, upload the cell growth protocol to the wiki, and link to the uploaded protocol file in the Protocol column. Then send the cell growth protocol to the NHGRI ENCODE team , who will forward it to the RWG. Once the protocol is approved by the Resources working group, it will be registered by the DCC and can be used in data submissions. For more information on editing wiki files, see the Help link in the navigation panel.

Note: To find an appropriate Term ID in the Brenda Tissue Ontology:

  • Go to the EBI Ontology Lookup page
  • Select BRENDA Tissue / enzyme source in the pull-down ontology list
  • Enter the cell type in the Term Name box and hit return. This should generate a list of hyperlinks to BTO terms.
  • Browse through the list of hyperlinks by (1) clicking on the hyperlink (which should take you back to the Ontology Lookup page) and (2) clicking the Browse button (which should take you to the BTO Ontology browser).
  • When you find an appropriate term, copy its URL from the BTO Ontology browser into Term ID column of the table below.

Cell Type Description Lineage Karyotype Sex Tissue URL for Ordering Term ID Submitting Lab (by PI) Protocol Approved|
Formatting Conventions: cell name "_" more specific details, donor ID, vendor ID, or lot ID (must be unique) non-redundant (leave out descriptions such as normal, human and sex), lower-case, comma separated phrases ectoderm, mesoderm, endoderm, inner cell mass or blank cancer or normal M, F or U general tissue source, lower-case "["website vendorName vendorID"]" (space-delimited, no quotes) "["ebiBrendaTissueWebsite BTO:termID"]" (space-delimited, no quotes) PI last name "["[pdfTitle verticalBarOrPipe cellName]"]" (space-delimited, no quotes) N/A
(Example) T-47D T-47D is a human epithelial cell line derived from an mammary ductal carcinoma, hypotriploid cancer F breast ATCC HTB-133 BTO:0001248 Myers T-47D N/A
(Example) NH-A (just updating protocol documents) Stam (upload document here) N/A
H0287-(test) EBV-transformed lymphoblastoid cell line (LCL) was derived from peripheral blood donated by a normal healthy male. mesoderm normal Male blood H0287 cells were obtained from the laboratory of Dr. Wendy Raskind, Department of Medicine, Division of Medical Genetics, University of Washington (also known as HCM287). BTO:0002062 Stam H0287 Yes

Registered Cell Types

The following Cell Types have been registered to the ENCODE validator, and can be used in data submissions: