Welcome to Mouse Encode Project at Ren Lab!

Data can be downloaded and viewed in ENCODE website. The raw data has also been deposited to GEO with the GEO accession ID GSE29184 .

Below are the links to the predicted cis-regulatory elements in each tissue/cell type. To map promoters, we relied exclusively on the presence of H3K4me3. To identify enhancers, we took advantage of the chromatin signature pattern that they share, i.e. the presence of H3K4me1 but absence of H3K4me3, and developed a chromatin-signature based enhancer predictor using the distal P300 binding sites in mESCs as training data set. To identify potential insulator elements, we determined the binding sites of CTCF in each tissue. For details, please refer to the the methods section of the paper.

Bone Marrow Cerebellum Cortex E14.5 brain E14.5 heart
E14.5 limb E14.5-liver Heart Intestine Kidney
Liver Lung MEF mESC Olfactory bulb
Placenta Spleen Testes Thymus

We also determined the transcriptome in each tissue or cell type through RNA-Seq experiments using a protocol that permits the detection of both abundance and strandedness of RNA transcripts. We mapped raw reads in FASTQ format to the mouse genome with TopHat software and the wig files were also generated by TopHat. We assigned expression value(FPKM) for each gene in RefSeq with Cufflinks software. Note, if you want to remap the RNA-Seq reads by yourself, please remove the first 6 bases(sequencing barcode) from the FASTQ files for samples in GSM8509XX series (SRR392604-SRR392619).

Download gene expression files for all 19 tissues

Download the RefSeq promoter usage (Supplemenatry table 4)

Download the predicted EPUs (Supplemenatry table 5)

Download the linked promoter and enhancer pairs in different tissues (Supplemenatry table 7)

Listed below are the tissue-specific enhancers used in Figure 4D and the downstream motif/Go term analysis. To cluster the enhancers, we first combined the predicted enhancers from all the tissue/cell types, and the progressively merged enhancers within 1.5 kb. The values in each bin in Figure 4D is the normalized H3K4me1 intensity for +-1.5 kb around the center of the predicted enhancers. Cluster 3.0 was used to generated the final heatmap.

Download the tissue-specific enhancers used in figure 4D