--------------------------------------------------------------- mm10.trackDb.html : Differences exist between hgwbeta and hgw2 (RR fields taken from public MySql server, not individual machine) 7880,13268d7879 < encode4RegEpigenetics | html < encode4RegEpigenetics |

Description

< encode4RegEpigenetics | < encode4RegEpigenetics |

This track displays genome-wide epigenomic signals from 1,178 individual ENCODE < encode4RegEpigenetics | experiments, including DNase-seq and ATAC-seq for chromatin accessibility, and ChIP-seq < encode4RegEpigenetics | for the histone modifications H3K4me3 and H3K27ac, as well as CTCF binding.

< encode4RegEpigenetics | < encode4RegEpigenetics |

DNase-seq and ATAC-seq identify regions of open chromatin commonly < encode4RegEpigenetics | associated with regulatory elements such as enhancers, promoters, and insulators.
ChIP-seq for the histone modifications H3K4me3 and H3K27ac mark active and poised promoters < encode4RegEpigenetics | and enhancers.
CTCF ChIP-seq reveals chromatin loop anchors and insulator elements.

< encode4RegEpigenetics | < encode4RegEpigenetics |

Each subtrack represents a single experiment in a specific biosample, displayed as a < encode4RegEpigenetics | bigWig signal track. These datasets provide the underlying experimental signals used to < encode4RegEpigenetics | generate the corresponding layered summary tracks. Additional datasets measuring < encode4RegEpigenetics | epigenomic signals are available at the < encode4RegEpigenetics | ENCODE portal.

< encode4RegEpigenetics |

This composite contains both signal (bigWig) and peak (bigBed) data for each experiment, < encode4RegEpigenetics | selectable via the "Data Type" facet in the track settings.

< encode4RegEpigenetics | < encode4RegEpigenetics |

Display Conventions and Configuration

< encode4RegEpigenetics | < encode4RegEpigenetics |

Click a specific biosample type and organ/tissue combination to view available datasets. < encode4RegEpigenetics | Subtracks can be further filtered by the epigenetic signal type (ATAC, DNase, CTCF, < encode4RegEpigenetics | H3K27ac, and H3K4me3) and life stage of the biosample. Each track is colored based on < encode4RegEpigenetics | the type of signal.

< encode4RegEpigenetics | < encode4RegEpigenetics |

Data Access

< encode4RegEpigenetics |

< encode4RegEpigenetics | The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the < encode4RegEpigenetics | Table Browser or the < encode4RegEpigenetics | Data Integrator. < encode4RegEpigenetics | For automated download and analysis, the genome annotation is stored in bigWig (signal) < encode4RegEpigenetics | and bigBed (peak) files that can be downloaded from < encode4RegEpigenetics | our download server. < encode4RegEpigenetics | The data may also be explored interactively using our < encode4RegEpigenetics | REST API. < encode4RegEpigenetics | The original data files are also available from the < encode4RegEpigenetics | ENCODE portal.

< encode4RegEpigenetics | < encode4RegEpigenetics |

< encode4RegEpigenetics | Signal files may be locally explored using bigWigToWig, e.g., < encode4RegEpigenetics |

< encode4RegEpigenetics | bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/10/16/d60aeb91-36d8-4d24-8d03-4c350a5f5ac3/ENCFF220DSP.bigWig stdout < encode4RegEpigenetics |

< encode4RegEpigenetics | Peak files may be explored using bigBedToBed, e.g., < encode4RegEpigenetics |

< encode4RegEpigenetics | bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/10/16/a1cbfde2-b570-4c32-8b0f-b1557de8849a/ENCFF209SYF.bigBed stdout < encode4RegEpigenetics |

< encode4RegEpigenetics | Instructions for downloading these tools can be found < encode4RegEpigenetics | here.

< encode4RegEpigenetics | < encode4RegEpigenetics |

Credits

< encode4RegEpigenetics | < encode4RegEpigenetics |

Data were generated by the ENCODE Consortium. We thank the production labs for generating < encode4RegEpigenetics | the data: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), John Stamatoyannopoulos (UW), Michael Snyder (Stanford), Richard Myers (HAIB), and Ross Hardison (PennState).

< encode4RegEpigenetics | < encode4RegEpigenetics |

The data were further processed for visualization through a collaborative effort between < encode4RegEpigenetics | the Weng lab and the < encode4RegEpigenetics | Moore lab at UMass < encode4RegEpigenetics | Chan Medical School (funded by NIH grant HG012343). Integration and visualization were < encode4RegEpigenetics | developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, < encode4RegEpigenetics | who were part of the ENCODE Data Analysis Center.

< encode4RegEpigenetics | < encode4RegEpigenetics |

References

< encode4RegEpigenetics | < encode4RegEpigenetics |

< encode4RegEpigenetics | ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, < encode4RegEpigenetics | Kawli T, Davis CA, Dobin A et al. < encode4RegEpigenetics | < encode4RegEpigenetics | Expanded encyclopaedias of DNA elements in the human and mouse genomes. < encode4RegEpigenetics | Nature. 2020 Jul;583(7818):699-710. < encode4RegEpigenetics | PMID: 32728249; PMC: PMC7410828 < encode4RegEpigenetics |

< encode4RegEpigenetics | < encode4RegEpigenetics |

< encode4RegEpigenetics | Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, < encode4RegEpigenetics | Fu Y et al. < encode4RegEpigenetics | < encode4RegEpigenetics | An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional < encode4RegEpigenetics | Regulation. < encode4RegEpigenetics | Nature. 2026 January 7. < encode4RegEpigenetics | PMID: 39763870; PMC: PMC11703161 < encode4RegEpigenetics |

Description

< encode4RegRnaSeq | < encode4RegRnaSeq |

This track displays genome-wide, strand-specific transcription levels from 1,054 < encode4RegRnaSeq | individual ENCODE total RNA-seq experiments. The data capture both coding and non-coding < encode4RegRnaSeq | RNAs profiled across all phases of the ENCODE project. The signal shown is derived from < encode4RegRnaSeq | the reads per million (RPM) of uniquely mapped reads on each genomic strand. The data < encode4RegRnaSeq | are processed following the < encode4RegRnaSeq | ENCODE < encode4RegRnaSeq | bulk RNA-seq pipeline.

< encode4RegRnaSeq | < encode4RegRnaSeq |

Each subtrack represents a single RNA-seq experiment in a specific biosample, with < encode4RegRnaSeq | separate signal tracks for the plus and minus strands. These datasets provide the < encode4RegRnaSeq | underlying experimental signals used to generate the corresponding layered summary tracks. < encode4RegRnaSeq | Additional datasets measuring transcription levels are available at the < encode4RegRnaSeq | ENCODE portal.

< encode4RegRnaSeq | < encode4RegRnaSeq |

Display Conventions and Configuration

< encode4RegRnaSeq | < encode4RegRnaSeq |

Subtracks are organized by strand (plus and minus strand views). Click a specific < encode4RegRnaSeq | biosample type and organ/tissue combination to view available datasets. Subtracks can be < encode4RegRnaSeq | further filtered by life stage of the biosample. Each track is colored based on the < encode4RegRnaSeq | organ/tissue of origin.

< encode4RegRnaSeq | < encode4RegRnaSeq |

Data Access

< encode4RegRnaSeq |

< encode4RegRnaSeq | The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the < encode4RegRnaSeq | Table Browser or the < encode4RegRnaSeq | Data Integrator. < encode4RegRnaSeq | For automated download and analysis, the genome annotation is stored in bigWig < encode4RegRnaSeq | files that can be downloaded from < encode4RegRnaSeq | our download server. < encode4RegRnaSeq | The data may also be explored interactively using our < encode4RegRnaSeq | REST API. < encode4RegRnaSeq | The original data files are also available from the < encode4RegRnaSeq | ENCODE portal.

< encode4RegRnaSeq | < encode4RegRnaSeq |

< encode4RegRnaSeq | These files may also be locally explored using our tool bigWigToWig, < encode4RegRnaSeq | which can be compiled from the source code or downloaded as a precompiled < encode4RegRnaSeq | binary for your system. Instructions for downloading source code and binaries can be found < encode4RegRnaSeq | here. < encode4RegRnaSeq | The tool can also be used to obtain data confined to a given range, e.g., < encode4RegRnaSeq |

< encode4RegRnaSeq | bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2021/05/24/2b7c3f15-8fca-4159-95e3-abe926455192/ENCFF046IVV.bigWig stdout

< encode4RegRnaSeq | < encode4RegRnaSeq |

Credits

< encode4RegRnaSeq | < encode4RegRnaSeq |

Data were generated by the ENCODE Consortium. We thank the production labs for generating < encode4RegRnaSeq | the data: Drs. Alexander Hoffmann (UCLA), Barbara Wold (Caltech), Manuel Garber (UMass), Michael Snyder (Stanford), Ross Hardison (PennState), and Thomas Gingeras (CSHL).

< encode4RegRnaSeq | < encode4RegRnaSeq |

The data were further processed for visualization through a collaborative effort between < encode4RegRnaSeq | the Weng lab and the < encode4RegRnaSeq | Moore lab at UMass < encode4RegRnaSeq | Chan Medical School (funded by NIH grant HG012343). Integration and visualization were < encode4RegRnaSeq | developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, < encode4RegRnaSeq | who were part of the ENCODE Data Analysis Center.

< encode4RegRnaSeq | < encode4RegRnaSeq |

References

< encode4RegRnaSeq | < encode4RegRnaSeq |

< encode4RegRnaSeq | ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, < encode4RegRnaSeq | Kawli T, Davis CA, Dobin A et al. < encode4RegRnaSeq | < encode4RegRnaSeq | Expanded encyclopaedias of DNA elements in the human and mouse genomes. < encode4RegRnaSeq | Nature. 2020 Jul;583(7818):699-710. < encode4RegRnaSeq | PMID: 32728249; PMC: PMC7410828 < encode4RegRnaSeq |

< encode4RegRnaSeq | < encode4RegRnaSeq |

< encode4RegRnaSeq | Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, < encode4RegRnaSeq | Fu Y et al. < encode4RegRnaSeq | < encode4RegRnaSeq | An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional < encode4RegRnaSeq | Regulation. < encode4RegRnaSeq | Nature. 2026 January 7. < encode4RegRnaSeq | PMID: 39763870; PMC: PMC11703161 < encode4RegRnaSeq |

Description

< encode4RegTfChip | < encode4RegTfChip |

This track displays genome-wide binding profiles of DNA-associated proteins from 334 < encode4RegTfChip | individual ENCODE ChIP-seq experiments. These proteins include transcription factors (TFs), < encode4RegTfChip | RNA polymerase, and chromatin-associated proteins involved in transcriptional regulation. < encode4RegTfChip | Sequence-specific TFs bind directly to DNA motifs via DNA-binding domains, while others < encode4RegTfChip | interact indirectly through protein-protein interactions. ChIP-seq (chromatin < encode4RegTfChip | immunoprecipitation followed by sequencing) enables genome-wide mapping of protein-DNA < encode4RegTfChip | interactions. Each subtrack represents an individual ChIP-seq experiment, showing signal < encode4RegTfChip | peaks that often correspond to protein binding sites in specific biosamples. Additional < encode4RegTfChip | ChIP-seq datasets can be explored through the < encode4RegTfChip | ENCODE portal.

< encode4RegTfChip |

This composite contains both signal (bigWig) and peak (bigBed) data for each experiment, < encode4RegTfChip | selectable via the "Data Type" facet in the track settings.

< encode4RegTfChip | < encode4RegTfChip |

Display Conventions and Configuration

< encode4RegTfChip | < encode4RegTfChip |

Click a specific protein target and organ/tissue combination to view available datasets. < encode4RegTfChip | Subtracks can be further filtered by the type and life stage of the biosample. Each peak < encode4RegTfChip | is displayed as a bigBed item, shaded in grayscale with intensity reflecting the ChIP-seq < encode4RegTfChip | signal strength.

< encode4RegTfChip | < encode4RegTfChip |

Data Access

< encode4RegTfChip |

< encode4RegTfChip | The ENCODE 4 Regulation data on the UCSC Genome Browser can be explored interactively with the < encode4RegTfChip | Table Browser or the < encode4RegTfChip | Data Integrator. < encode4RegTfChip | For automated download and analysis, the genome annotation is stored in bigWig (signal) < encode4RegTfChip | and bigBed (peak) files that can be downloaded from < encode4RegTfChip | our download server. < encode4RegTfChip | The data may also be explored interactively using our < encode4RegTfChip | REST API. < encode4RegTfChip | The original data files are also available from the < encode4RegTfChip | ENCODE portal.

< encode4RegTfChip | < encode4RegTfChip |

< encode4RegTfChip | Signal files may be locally explored using bigWigToWig, e.g., < encode4RegTfChip |

< encode4RegTfChip | bigWigToWig -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/11/24/559f88bd-29ea-4694-9cdf-3eddf3d87e0e/ENCFF265VZJ.bigBed stdout < encode4RegTfChip |

< encode4RegTfChip | Peak files may be explored using bigBedToBed, e.g., < encode4RegTfChip |

< encode4RegTfChip | bigBedToBed -chrom=chr1 -start=100000 -end=100500 https://encode-public.s3.amazonaws.com/2020/11/24/559f88bd-29ea-4694-9cdf-3eddf3d87e0e/ENCFF265VZJ.bigBed stdout < encode4RegTfChip |

< encode4RegTfChip | Instructions for downloading these tools can be found < encode4RegTfChip | here.

< encode4RegTfChip | < encode4RegTfChip |

Credits

< encode4RegTfChip | < encode4RegTfChip |

Data were generated by the ENCODE Consortium. We thank the production labs for generating < encode4RegTfChip | the data: Drs. Barbara Wold (Caltech), Bing Ren (UCSD), Christine Disteche (UW), Michael Snyder (Stanford), Richard Myers (HAIB), and Ross Hardison (PennState).

< encode4RegTfChip | < encode4RegTfChip |

The data were further processed for visualization through a collaborative effort between < encode4RegTfChip | the Weng lab and the < encode4RegTfChip | Moore lab at UMass < encode4RegTfChip | Chan Medical School (funded by NIH grant HG012343). Integration and visualization were < encode4RegTfChip | developed by Drs. Mingshi Gao, Jill Moore, and Zhiping Weng at UMass Chan Medical School, < encode4RegTfChip | who were part of the ENCODE Data Analysis Center.

< encode4RegTfChip | < encode4RegTfChip |

References

< encode4RegTfChip | < encode4RegTfChip |

< encode4RegTfChip | ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, < encode4RegTfChip | Kawli T, Davis CA, Dobin A et al. < encode4RegTfChip | < encode4RegTfChip | Expanded encyclopaedias of DNA elements in the human and mouse genomes. < encode4RegTfChip | Nature. 2020 Jul;583(7818):699-710. < encode4RegTfChip | PMID: 32728249; PMC: PMC7410828 < encode4RegTfChip |

< encode4RegTfChip | < encode4RegTfChip |

< encode4RegTfChip | Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, < encode4RegTfChip | Fu Y et al. < encode4RegTfChip | < encode4RegTfChip | An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional < encode4RegTfChip | Regulation. < encode4RegTfChip | Nature. 2026 January 7. < encode4RegTfChip | PMID: 39763870; PMC: PMC11703161 < encode4RegTfChip |