NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
Mouse cell and tissue metadata
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 (email@example.com), as well as the DCC mailing list (firstname.lastname@example.org) 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.
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: