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.

TF ChIP-seq
This composite track displays signals and peak calls for selected, published transcription factor (TF) ChIP-seq experiments in human blood cells, with a heavy emphasis on erythroid cells, or a related cell line, K562. The datasets were selected based on the known roles of the TFs in erythroid gene regulation and chromatin organization as well as manual inspection of data quality. The data were generated in several laboratories and published in many different papers, using a variety of approaches to obtain the erythroid cells, most often erythroblasts. Details on the sources of the data are in the following table.

Display Conventions and Configuration

Users can choose the tracks to display using the check boxes in the matrix of TFs and cell types or the list of tracks. The pull-down menus at the top of the page allow choices to examine peak calls or signal tracks. The signal for data obtained directly from the ENCODE data portal on K562 cells are shown as "Fold-change" and other signal intensity data are shown as "Signal". Parameters for track configurations, including y-axis settings, are accessed by clicking the down arrow for "Peaks", "Signal", or "Fold-change".

Methods

ChIP-seq data on the selected TFs in erythroid cells and neutrophils were downloaded from GEO and SRA, and the reads were mapped to the human GRCh38 genome assembly using the VISION project pipeline (Xiang et al., 2020), which is similar to the ENCODE pipeline except the mapping retains multi-mapped reads. The data processed through the VISION pipeline have track names starting with a number such as 100179 (an internal VISION id). The ChIP-seq signal data on selected TFs in K562 were downloaded directly from the ENCODE data portal; these tracks have names starting with the id ENCFF.

Credits

The data downloads, re-mapping and processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine. Data to include was selected and curated by Ross Hardison.

References

Heuston EF, Keller CA, Lichtenberg J, Giardine B, Anderson SM; NIH Intramural Sequencing Center; Hardison RC, Bodine DM. Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points. Epigenetics Chromatin. 2018 May 28;11(1):22. PMID: 29807547; PMCID: PMC5971425.

Xiang G, Keller CA, Heuston E, Giardine BM, An L, Wixom AQ, Miller A, Cockburn A, Sauria MEG, Weaver K, Lichtenberg J, Göttgens B, Li Q, Bodine D, Mahony S, Taylor J, Blobel GA, Weiss MJ, Cheng Y, Yue F, Hughes J, Higgs DR, Zhang Y, Hardison RC. An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis. Genome Res. 2020 Mar;30(3):472-484. PMID: 32132109; PMCID: PMC7111515.

Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Göttgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. Genome Res. 2024 Aug 20;34(7):1089-1105. PMID: 38951027; PMCID: PMC11368181.

Data Release Policy

These ChIP-seq data are available for use without restrictions.

Contact

Ross Hardison rch8@psu.edu