RNA-seq This composite track displays RNA-seq signal data from multiple human hematopoietic cell types as part of the VISION project (ValIdated Systematic IntegratiON of hematopoietic epigenomes). The data provide a genome-wide view of transcriptional activity across blood cell types, complementing the epigenomic data used for chromatin state analysis in the VISION project.
The RNA-seq data were generated by the Blueprint Epigenome Consortium and other published studies. Cell types represented include hematopoietic stem cells (HSC), multipotent progenitor cells (MPP), common myeloid progenitors (CMP), megakaryocyte-erythroid progenitors (MEP), granulocyte-monocyte progenitors (GMP), common lymphoid progenitors (CLP), erythroblasts (ERY), megakaryocytes (MK), eosinophils (EOS), monocytes (MON), neutrophils (NEU), B cells, natural killer cells (NK), CD4+ T cells, and CD8+ T cells. Data from the immortalized cell lines HUDEP-1 and HUDEP-2 are also included.
In "full" mode, the signal is displayed as a continuous variable along the chromosomes. The tracks include both unique and multi-mapped signal for stranded and unstranded RNA-seq libraries from the Blueprint processing pipeline (STAR/RSEM).
The track names include donor identifiers from the Blueprint Consortium, the RNA-seq library type (stranded or unstranded, plus or minus strand, unique or multi-mapping), and the cell type.
RNA-seq data were downloaded from the data portal of the Blueprint Epigenome Consortium (Adams et al. 2012) and other published sources. Reads were aligned using STAR and quantified using RSEM through the Blueprint processing pipeline. Signal tracks represent genome-wide coverage of mapped reads.
The data downloads, 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, 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 data are available for use without restrictions.
Ross Hardison rch8@psu.edu