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+ ++We are pleased to announce a new ENCODE Expression track container for the +mouse mm10/GRCm38 and +mm39/GRCm39 assemblies. The container shows bulk RNA-seq gene +expression across mouse embryonic development, produced by the +Wold Lab at Caltech as part +of the ENCODE project and +described in He +et al., Nature 2020. These tracks are turned on by default on +both assemblies, so you will see them the next time you open the mouse browser. +
+ ++The data cover 17 tissues and organs sampled at up to eight developmental time points, +from embryonic day 10.5 through embryonic day 16.5 and at birth (P0), with two +biological replicates at each point. That gives 78 tissue and time point combinations +and 156 samples in total. +
+ ++Expression is shown as a bar chart at each gene, with one bar per sample. Bars are +colored by tissue, and the shade darkens as development advances, so you can see a +tissue's trajectory over time at a glance. You can filter the bars by tissue and time +point from the track configuration page, which is useful for comparing a small number +of tissues without the rest of the series in the way. +
+ +Expression of Gap43 across the developmental time course on +mm10. Each bar is one sample, colored by tissue and darkening with developmental age. +Expression rises through development and is highest in the four neural tissues on the +right of the chart.
++Expression values were generated by RSEM from the ENCODE long RNA-seq pipeline, and are +provided in two units against two GENCODE annotation sets. The units are TPM, or +transcripts per million, and FPKM, or fragments per kilobase of exon per million mapped +fragments. +
++The mm39 tracks were lifted from the mm10 GENCODE M21 data, since GENCODE M21 +predates the GRCm39 assembly. Of the 55,536 genes in the mm10 data, 55,447 lifted +successfully. For details, see the individual track description pages, as well +as the publication The changing mouse embryo transcriptome at whole tissue and +single-cell resolution. +
+ + ++Thanks to Peng He, who led the analysis, and to Diane Trout at the Wold Lab, who +managed the data and built the original track hub. Thanks also to Barbara Wold and the +Wold Lab, the ENCODE +Consortium and the ENCODE Data Coordination Center for generating and processing +the underlying experiments, and to Brittney Wick for the sample color scheme shared +with the UCSC Cell Browser. These tracks were built and reviewed at UCSC by Gerardo +Perez, Max Haeussler and Lou Nassar. +
+We are pleased to announce faceted composites, a new interface for composite tracks that hold very large numbers of subtracks. The standard composite works well for about 20 to 50 subtracks, but it becomes unwieldy once the count reaches the hundreds or thousands. A faceted composite is an alternative display for those cases: facets along the left side filter the collection, while a paginated table on the right lists the matching subtracks, letting users narrow thousands of entries down to the handful relevant to their work. The individual-experiment tracks in the ENCODE4 Regulation collection, announced in July 2026, already use this interface. Faceted composites are configured entirely through trackDb settings, so any hub developer can build one.