ErythronDB

The original ErythronDB site is now retired!

Code for generating the web site is available here.

The Erythron Database (ErythronDB) was a resource dedicated to facilitating better understanding of the cellular and molecular underpinnings of mammalian erythropoiesis. It provided a searchable database of murine gene expression during murine primitive, definitive, and stress erythroid cells at progressive stages of maturation. ErythronDB also allowed users to explore the role of erythropoietin (the principal hormone regulating erythropoiesis) and identify potential targets of EPO-signaling via comparison of rhEPO-treated versus control cells in mouse (microarray expression) and human (proteomics) datasets.

ErythronDB was developed by a team of researchers at the University of Pennsylvania.

Datasets in ErythronDB

Ontogeny of erythroid gene expression

• Comparison of global gene expression in primitive, fetal definitive, and adult definitive erythroid cells at morphologically equivalent stages of maturation purified from embryonic, fetal, and adult mice to delineate the gene anatomy of differentiating primary primitive and definitive red blood cells (RBCs).
• Organism: Mm
• Submitter: James Palis
• Primary publication: Kingsley PD et al. 2013. Ontogeny of erythroid gene expression. Blood. 121:e5-e13. PMID: 23243273
• Accession: E-MTAB-1035

EPO-regulated targets in murine erythroid progenitors

• Global gene expression profiling of bone marrow-derived erythroid progenitor cells at E1 (CFU-e), E2 (proerythroblasts), and E3 (maturing erythroblast) stages of development under stress erythropoiesis conditions and in response to EPO challenge. MACS-isolated E1, E2, and E3 stage EPCs were cultured in SP34ex media for 6 hrs in the absence of hematopoietic growth factors and the presence of insulin (to enforce survival and anti-apoptotic effects) and then exposed to rhEPO for 90 minutes. Gene expression analysis was performed using Affymetrix Mouse Genome 430 2.0 arrays; microarray data were analyzed using Bioconductor.
• Organism: Mm
• Submitter: Don Wojchowski
• Accession: E-MTAB-5373

EPO-regulated targets in murine E1 cells with a truncated erthropoietin receptor (EpoR)

• Global gene expression profiling of bone marrow-derived erythroid progenitor cells at E1 (CFU-e) with wild type and truncated EpoR-H alleles under stress erythropoiesis conditions and in response to EPO challenge. MACS-isolated E1 stage EPCs were cultured in SP34ex media for 6 hrs in the absence of hematopoietic growth factors and the presence of insulin (to enforce survival and anti-apoptotic effects) and then exposed to rhEPO for 90 minutes. The EpoR-H mouse strain was obtained by using homologous recombination to delete the distal 108 amino acids of the EpoR in ES cells.
• Organism: Mm
• Submitter: Don Wojchowski
• Protocol overview: To isolate E1 erythroid progenitors cells, expanded cells were depleted of Lin+ cells (via MACS microbead procedures, Miltenyi). EPCs were then isolated by MACS-based positive selection (Kit high/CD71 high/Ter119-).

EPO phosphorylation PTM targets in UT-7epo-E cells

• Using a human EPO-dependent UT-7epo-E erythroid progenitor cell model, phospho-PTM LC-MS/MS was employed to document EPOR/JAK2 regulated phospho-PTM events. Experiments involved a short-term EPO challenge (after first withdrawing EPO from the UT-7epo-E cells) after which total cellular protein was then extracted, and hydrolyzed using trypsin or Glu-C. Peptides modified at p-Y or p-TPP motifs were the retrieved via immunoadsorption and LC-MS/MS employed to define peptide sequences and sites and levels of EPO-mediated phosphorylation. Data are also available for PTM-targets of hematide exposure.
• Organism: Hs
• Submitter: Don M. Wojchowski
• Primary publication: Held MA et al. 2020. Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis. Exp Hematol. 2020 Apr;84:29-44. PMID: 32259549

To Cite this Resource

Kingsley P.D., Greenfest-Allen E., Frame J., Bushnell T., Malik J., McGrath K.E., Stoeckert C.J., and Palis J. Ontogeny of erythroid gene expression. eBlood. 2012. PMID: 23243273

Funding

National Institute of Diabetes and Digestive Kidney Diseases (Erythroid Lineage Molecular Toolbox); NIDDK R01 DK 071116