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Mouse Metadata

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All metadata describing ENCODE experiments must be registered in the DCC controlled vocabularies before data can be submitted. The specific metadata types needed for each experiment type is decided jointly by the production lab and the DCC data wrangler, as part of the data agreement. Mouse ENCODE experiments should reuse applicable terms from the human ENCODE project, listed here:

Commonly used vocabularies are:

Additional vocabularies developed for mouse experiments will include:


Strain

Term Description
CD-1 Strain CD-1. Multipurpose mouse used for safety and efficacy testing, aging, surgical model, pseudopregnancy.
C57BL/6 C57 black 6, the most common inbred strain of laboratory mouse
129 Strain 129, has widely available embryonic stem cells
C3H Strain C3H, very related to C57Bl
B10.H-2aH-4bp/Wts Derived by inbreeding from selected F2 progeny of B10.A X B10.129
Spretus.BL6-Xist M.spretus x C57BL/6J hybrid mouse such that the C57Bl/6J X chromosome (maternal) is always the inactive X.
Unknown Unknown strain origin
BALB/cJ BALB/cJ is a common inbred strain of laboratory mouse.
129.DLCR/DLCR 129 strain mouse with homozygous deletion of the beta-globin LCR region, see Bender et. al. (2000). Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Mol. Cell 5, 387–393.

Registered Strains

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=/usr/local/apache/cgi-bin/encode/cv.ra&type=strain{scrolling=auto}{height=400}</embedurl>

Age

Term Stage Description
E11.5 Embryonic Embryonic day 11.5
E13.5 Embryonic Embryonic day 13.5
E14 Embryonic Embryonic day 14
E14.5 Embryonic Embryonic day 14.5
E18 Embryonic Embryonic day 18
E18.5 Embryonic Embryonic day 18.5
adult-4wks Adult Adult 4wks
adult-5wks Adult Adult 5wks
adult-8wks Adult Adult 8wks
adult-10-12wks Adult Adult 10-12wks
E0 Embryonic Embroyonic stem cell age
immortalized Cell Line Immortal cells
adult-1wk Adult Adult 1wk
newborn Adult Newborn

Registered Ages

<embedurl>http://hgwdev.cse.ucsc.edu/cgi-bin/hgEncodeVocab?ra=/usr/local/apache/cgi-bin/encode/cv.ra&type=age{scrolling=auto}{height=300}</embedurl>

Mouse cell lines and tissues

Mouse cell lines, tissues, and primary cells are registered by clicking on the link above.