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Mouse cell and tissue metadata

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Registering mouse cell and tissue metadata for ENCODE use

All cell lines, primary cells, and tissues used in ENCODE experiments must be added to the DCC controlled vocabulary for cell types before data can be submitted for that cell type. The information needed for registration includes: a unique identifier ('Term'), some basic metadata (see below), and the growth/harvest protocol used. To do this, post the information in table, below, and notify Melissa Cline at UCSC (cline@soe.ucsc.edu), as well as the DCC mailing list (encode@soe.ucsc.edu) in order to complete the registration process. Registered cell/tissue types will be displayed in a separate section on this page, below the wiki tables used for entering them.

Registration table

Fill in one row in the table for each cell type or tissue that will be used, using the following guidelines:

Term Unique identifier
Description e.g mouse embryonic stem cells, spleen
Category T (tissue) or L (cell line ) or P (primary cells)
Ontology Link Selected from Mouse Anatomical Dictionary
Sex M, F or U (unknown)
Source Supplier and catalog # linked to ordering URL (for cell lines)
Submitting Lab PI last name
Protocol Link to uploaded protocol file (culture or harvest)

The 'Term' should be the shortest recognizable identifier for the cell/tissue type, and should avoid special characters. Special characters that may be used if necessary: hyphen(-), underscore(_), plus(+). To upload the protocol file, use the 'upload file' link in left menu 'toolbox'. The first row in this table is an example from the human ENCODE cell type vocabulary, included as an example.

Term Description Category Ontology Link Sex Source Submitting Lab Protocol



Registered Cell Types

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

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=/usr/local/apache/cgi-bin/encode/cv.ra&type=Cell+Line&organism=Mouse{scrolling=auto}{height=900}</embedurl>