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.
RNA-seq This composite track displays signal levels for stable transcripts across the genomes of human blood cells, including both multilineage progenitor cells and mature cells.
Most of the data displayed were selected from resources at the data hub for the Blueprint project consortium (Adams et al. 2012). If possible, RNA-seq data on each cell type were gathered from two different donors. The donor id is the string at the beginning of each track name. Depending on the cell type, the RNA-seq data were either unstranded, denoted by "RNAUnstranded" in the track name, or stranded, which generates two tracks from each experiment, with either "RNAPlus" or "RNAMinus" in the track name for the plus strand or minus strand signals, respectively. In these cases, the signal is always positive even for the minus strand. Further, the data processing center for Blueprint mapped the RNA-seq reads in two different modes, either including reads that map to multiple locations, indicated by "Multi" in the track name, or excluding the multi-mapping reads, which is indicated by the absence of "Multi" in the track name. Tracks from both types of RNA-seq protocols and from both mapping modes are included in this composite track.
RNA-seq data from three cell types, erythroblasts from in vitro differentiation of CD34+ cells (CD34+ ERY) and the two cell lines HUDEP-1 and HUDEP-2, were generated in Yong Cheng's lab and published as part of the integrative analysis in Xiang et al. 2024. These RNA-seq experiments generated stranded data, and the signal from the minus strand is shown as negative values.
The RNA-seq data from the Blueprint project consortium are shown as green tracks. The data from Yong Cheng's lab are shown as black tracks. Because of the mix of types of data, the default display for this composite track is set to "auto-scale to data view".
Users can choose the cell types for which to display the RNA-seq data using the check boxes in the list of cell types. For all cell types from the Blueprint project, users can select results from including ("Multi" in track name) or excluding reads that map to multiple locations in the genome.
The Blueprint data is displayed by linking to files at the Blueprint project data portal. The reads from the RNA-seq expeiments were aligned to the human genome using STAR and the results analyzed using RSEM.
The data downloads, re-mapping and processing, generation of the tracks displayed, and development of the track hub were done by Belinda Giardine.
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, Bock C, Boehm B, Campo E, Caricasole A, Dahl F, Dermitzakis ET, Enver T, Esteller M, Estivill X, Ferguson-Smith A, Fitzgibbon J, Flicek P, Giehl C, Graf T, Grosveld F, Guigo R, Gut I, Helin K, Jarvius J, Küppers R, Lehrach H, Lengauer T, LernmarkA, Leslie D, Loeffler M, Macintyre E, Mai A, Martens JH, Minucci S, Ouwehand WH, Pelicci PG, Pendeville H, Porse B, Rakyan V, Reik W, Schrappe M, Schübeler D, Seifert M, Siebert R, Simmons D, Soranzo N, Spicuglia S, Stratton M, Stunnenberg HG, Tanay A, Torrents D, Valencia A, Vellenga E, Vingron M, Walter J, Willcocks S. BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012 Mar 7;30(3):224-6. doi: 10.1038/nbt.2153. PMID: 22398613.
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.
These ChIP-seq data are available for use without restrictions.
Ross Hardison rch8@psu.edu