Gene Expression and Epigenetic Datasets

Helpful websites for querying gene expression and epigenetic changes in primary mouse and human hematopoiesis

1. Bloodspot

Curated database of mRNA Gene expression profiles, database of healthy and malignant hematopoiesis with purified and single cell mRNA sequencing profiles.

Bagger at al. (Porse). HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis. Nucleic Acids Research, 2013.

Bagger et al. (Rapin). BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles. Nucleic Acids Research, 2019.

2. Gene Expression Commons, Riken

Gene expression from many cells types including murine HSPC populations. You need to register to use the database, but it is free.

Seita et al. (Weissman). Gene Expression Commons: an open platform for absolute gene expression profiling. PLoS One, 2012, 7(7):e40321.

3. Single cell RNA-seq expression in primary human CMP, MEP, MKP and ERP

Lu et al. (Krause). The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Rep, 2018, 25(8):2083-2093.

4. Gene expression in primary human hematopoietic subpopulations

Hay et al (Salomonis). The Human Cell Atlas Bone Marrow Single-Cell Interactive Web Portal. Experimental Hematology, 2018.

5. Single cell analysis of the murine hematopoietic niche

Tikhonova et al. (Aifantis). The bone marrow microenvironment at single-cell resolution. Nature, 2019, 569.

6. Mouse Bone Marrow Stroma in Homeostasis - scRNA-seq of bone marrow stroma and its perturbation during malignancy (defines 17 stromal subsets)

Baryawno et al. (Scadden). A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia. Cell, 2019.

7. Another way to view “Scadden-Stromal.db” database established by Nathan Salomonis

8. Single cell seq analysis of primary human cells from hemogenic endothelium to birth

Calvanese et al. (Mikkola). Mapping human haematopoietic stem cells from haemogenic endothelium to birth. Nature, 2022.

9. The Transcriptional Landscape of Hematopoietic Stem Cell Ontogeny (Daley lab)

McKinney-Freeman et al. (Daley). The Transcriptional Landscape of Hematopoietic Stem Cell Ontogeny. Cell Stem Cell, 2012.

10. Blueprint

Many healthy donor and diseased samples profiled for multiple levels of readouts—although the portal is not intuitive to navigate. Expansive database with transciptomic/epigenomic analysis (RNA-seq, DNAme-seq, DNAseI-seq, 8 different ChIP-seq) on bone marrow, blood, cord blood, liver, tonsil, lymph node, thymus and cell lines.