Description:

The VISION Project
The VISION project conducted a ValIdated Systematic IntegratiON of epigenetic datasets across progenitor and differentiated blood cell types in mouse and human (Heuston et al. 2018, Xiang et al. 2020, Xiang et al. 2024). The project was carried out by an international group of scientists funded by the National Institute of Diabetes, Digestive, and Kidney Diseases of the National Institutes of Health (grant R24DK106766) and with intramural support from the National Human Genome Research Institute. Key products and results of the project can be visualized on the UCSC Genome Browser using this track hub. The project website provides other servers, databases, and data downloads.

Blacklists
Sequencing reads from ChIP-seq experiments accumulate above expectation both in genomic intervals associated with the target antigen (occupied by a transcription factor or in chromatin with a particular histone modification) and in unexpected intervals that generate a high signal in many ChIP-seq datasets. The high accumulations of reads in the latter intervals are artifacts of the assay, in some cases resulting from having a DNA sequence similar to the parts of the genome that are missing from reference genome assemblies. These genomic intervals with an artifactual excess of reads mapping to them are usually excluded from functional genomics analyses by placing them in a "blacklist" that is used to remove intervals from further consideration.

This composite track allows visualization of two sets of blacklists.

• One was developed by the ENCODE Project Consortium using the mouse mm9 assembly. We used liftOver to migrate the blacklisted intervals to the mm10 assembly.
• One is a composite made up of several components. It has the ENCODE blacklist, a mitochondrial blacklist from Peng He (B. Wold lab), and the blacklist regions from Penn State. The Penn State part was developed in the Hardison lab at Penn State from the input signal (no antibody treatment) from each of several mouse cell lines. This blacklist contains peaks called by MACS on the input signal and windows with a high signal. The high signal was defined by a 5,000 base pair sliding window with an average signal 4 fold greater than the genome average and a maximum score of at least 8 fold greater. The composite track contains a union and merge of all the cell specific blacklist regions. This was computed on the mm10 reference sequence that includes unplaced scaffolds but not alternate chromosomes.

Display Conventions and Configuration

Each track shows a black rectangle for each blacklisted genomic interval. Closely spaced blacklist intervals may be more distinguishable from each other in pack mode.

Methods

Methods for the ENCODE blacklist are given in Amemiya et al. (2019). The Hardison lab blacklist is described in Pimkin et al. (2014)

Credits

Belinda Giardine generated the tracks displayed and developed the track hub.

References

Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Sci Rep. 2019 Jun 27;9(1):9354. doi: 10.1038/s41598-019-45839-z. PMID: 31249361; PMCID: PMC6597582.

Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Res. 2014 Dec;24(12):1932-44. doi: 10.1101/gr.164178.113. Epub 2014 Oct 15. PMID: 25319996; PMCID: PMC4248311.

Data Release Policy

These data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu