52ebb985f6e3658f463e971b7acd4c3959d36f92
gperez2
Wed Apr 22 17:38:06 2026 -0700
Enlarged classification diagram (40% to 60%) on the cCRE registry
and Core Collection description pages. Updated the shortLabels on
all 90 Core Collection subtracks with biosample + age + assay
labels. refs #37131
diff --git src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
index 88defafdefa..d6c09ea03ca 100644
--- src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
+++ src/hg/makeDb/trackDb/mouse/mm10/cCREregistry.html
@@ -67,31 +67,31 @@
Candidate cis-regulatory elements (cCREs) were first anchored on nucleosome-sized DNase
hypersensitive sites (rDHSs) identified from DNase-seq data. These rDHSs were then annotated
using ChIP-seq data for histone modifications (H3K4me3 and H3K27ac, marking promoters and
enhancers, respectively) and CTCF, marking insulators. To supplement rDHS-anchored cCRE
definitions, transcription factor ChIP-seq peaks were incorporated, enabling identification
of cCREs even in regions of low chromatin accessibility. Although not used for anchoring,
ATAC-seq data were used to assess chromatin accessibility in biosamples lacking DNase-seq.
Because ATAC-seq was not standardized across all biosamples, the ATAC max-Z score is not included
in the registry bigBed fields or mouseOver. Only the four core assays (DNase, H3K4me3, H3K27ac,
and CTCF) are reported as max-Z scores. ATAC-seq signal tracks are available in the
ENCODE4 Regulation track.
The following diagram illustrates the biochemical signal patterns used to classify each cCRE type:
-
+
Data Access
The ENCODE accession numbers of the constituent datasets at the ENCODE Portal are available from the cCRE details page.
The data in this track can be interactively explored with the Table Browser or the Data Integrator. The data can be accessed from
scripts through our API,
the track name is "cCREregistry".
For automated download and analysis, this annotation is stored in a bigBed file
that can be downloaded from our download server.