ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501780/SRR501780_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501777/SRR501777_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501779/SRR501779_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501773/SRR501773_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501774/SRR501774_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501774/SRR501774_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501775/SRR501775_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501778/SRR501778_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501781/SRR501781_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501772/SRR501772_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501776/SRR501776_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501779/SRR501779_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501775/SRR501775_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501777/SRR501777_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501781/SRR501781_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501780/SRR501780_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501778/SRR501778_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501772/SRR501772_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501773/SRR501773_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR501/SRR501776/SRR501776_1.fastq.gzprimaryOK200GenomicsUniversity of California, San Diegohttps://www.ebi.ac.uk/ena/browser/view/PRJNA150507Mus musculusAs the most widely used mammalian model organism, mice play a critical role in biomedical research for mechanistic study of human development and diseases. Today, functional sequences in the mouse genome are still poorly annotated a decade after its initial sequencing. We report here a map of nearly 300,000 cis-regulatory sequences in the mouse genome, representing active promoters, enhancers and CTCF binding sites in a diverse set of 19 tissues and cell types. This map provides functional annotation to nearly 11% of the genome, and over 70% of conserved, non-coding sequences. We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that cis-regulatory sequences are organized into domains of coordinately regulated enhancers and promoters. Our results provide a valuable resource for the annotation of functional elements in the mammalian genome, and study of regulatory mechanisms for tissue-specific gene expression. Overall design: Cortex Hi-C experiment were conducted in biological replicatesxref:PubMed:22763441ENAfalseMus musculusA draft map of cis-regulatory sequences in the mouse genome [HiC]2025-09-242013-06-27PRJNA150507GSE345871009022763441