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p://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/SRR392430/SRR392430.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/SRR207059/SRR207059.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR505/SRR505018/SRR505018.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/SRR392335/SRR392335.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR505/SRR505025/SRR505025.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/SRR392361/SRR392361.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/SRR207047/SRR207047.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/SRR392328/SRR392328.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/SRR207073/SRR207073.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR392/SRR392354/SRR392354.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR207/SRR207066/SRR207066.fastq.gzprimaryOK200GenomicsUniversity of California, San Diegohttps://www.ebi.ac.uk/ena/browser/view/PRJNA142963Mus 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: 19 tissues and primary cell types were examined.xref:PubMed:22763441ENAHITS-CLIP, High Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, ahl4, ChIP-Chip, MUTYH-Associated Polyposis, Chromatin Immuno-precipitation, methionine aminopeptidase activity, Laboratory, Mus domesticus, Cross Linking and Immunoprecipitation Followed by Deep Sequencing, MYH-associated polyposis, mouse, autosomal recessive familial adenomatous polyposis, Maps, ChIP Sequencing, CLIP-Seq, Assay for Transposase-Accessible Chromatin Using Sequencing, 2610511A05Rik, ChIP-PET, House Mouse, ChIP-Exo, BB234005, House, Mus, Cis, CIS, G18, Chromatin Immunoprecipitation Sequencing-Chip, Mus musculus domesticus, 2, High-Throughput Sequencing of RNA Isolated by Crosslinking Immunoprecipitation, Mice, familial adenomatous polyposis, MAP, peptidase M activity, autosomal recessive, adenomas, Mus musculus, RUTBC3, rabGAPLP, CIS-1, Chromatin Immunoprecipitation Sequencing Chip, L-methionine aminopeptidase activity, Chromatin Immuno precipitation Sequencing, Genomes, Swiss, ChIP, mice, Chromatin Immunoprecipitation Paired End Tag, familial adenomatous polyposis 2, Chromatin Immuno Precipitation Paired End Tag, Swiss Mouse, Cross-Linking and Immunoprecipitation Followed by Deep Sequencing, RabGAP-5, Chromatin Immunoprecipitation, 9030605P22Rik, House Mice, Swiss Mice, Chromatin Immuno-precipitation Sequencing, whole genome, ChIP Exonuclease, MYH-Associated Polyposis, ChIP-Seq, Sequencing, Assay for Transposase Accessible Chromatin Using Sequencing, RABGAP5, domesticus, Laboratory Mice, autosomal recessive multiple colorectal adenomas, Chromatin Immunoprecipitation Paired-End Tag, SOCS, RUSC3, ChIA-PET., Chromatin Immuno-Precipitation Paired-End Tag, multiple colorectal, ATAC-Seq, Chromatin Immunoprecipitation Sequencing-Chips, Protein G18, MAP syndrome, Mouse, house mouse, Suppressor of cytokine signaling, ChIP-Exonuclease, Laboratory Mouse, BACTS2, FAP2, colorectal adenomatous polyposisMus musculus, Laboratory Mice., House, Mus, Laboratory, Swiss, Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, mouse <Mus musculus>, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, mice C57BL/6xCBA/CaJ hybrid, domesticus, Mus muscarisfalseMus musculusA draft map of cis-regulatory sequences in the mouse genome [ChIP-Seq]2025-09-242013-05-31PRJNA142963GSE292181009022763441