The ENCODE project has established an epigenomic resource for mammalian development, profiling a diverse panel of mouse tissues at eight developmental stages from 10.5 days post conception until birth.
This track set presents the results of a comprehensive study of chromatin state across these developmental stages, based on 1,128 ChiP-seq assays of 8 histone modifications in 12 tissues, performed by the laboratory of Bing Ren as part of the ENCODE Consortium, phase 3.
Histone modifications are post-translational chemical modifications (e.g. methylation, acetylation) of histone proteins present in chromatin. Histone modifications are core components of a cell's epigenome, and influence gene expression by modulating the activity of DNA sequences.
This track is a multi-view composite track that contains two data types (views). For each view, there are multiple subtracks that display individually on the browser. Instructions for configuring multi-view tracks are here. The views in this track are:
Peaks displayed in this track set are replicated peaks called with the Irreproducible Discovery Rate (IDR) framework These peaks are identical to those in the "replicated peaks" files on the ENCODE data portal. Signals displayed in this track correspond to the "fold change over control" files from merged replicates, reflecting the fold enrichment of ChIP signal over the input control. Data for individual replicates are available through the ENCODE portal.
Tracks are colored by histone modification. The table below list shows the assigned track color and the genomic region type and activity level characteristic of each modification.
Modification | Color | Regions | Activity Level | ||
---|---|---|---|---|---|
H3K4me3 | dark blue | promoters | active, poised | ||
H3K4me2 | royal blue | promoters, enhancers | active, poised | ||
H3K4me1 | light blue | enhancers | active, poised | ||
H3K27ac | dark green | promoters, enhancers | active | ||
H3K9ac | light green | promoters, enhancers | active | ||
H3K36me3 | gold | exons | active | ||
H3K27me3 | dark red | introns, intergenic | repressed | ||
H3K9me3 | light red | heterochromatin | repressed |
Data from this and all phases of ENCODE are publicly available through the ENCODE portal. The specific experiments included in this track set are listed here.
Gorkin et al. An atlas of dynamic chromatin landscapes in the developing mouse fetus. Nature, In Press. (pre-print: doi: https://doi.org/10.1101/166652)
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT et al. ENCODE data at the ENCODE portal. Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. PMID: 26527727; PMC: PMC4702836
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012 Aug 2;488(7409):116-20. PMID: 22763441; PMC: PMC4041622