BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles
Open accessAbstract
BloodSpot is a gene-centric database of mRNA expression of haematopoietic cells. The web-based interface to the database includes three concomitant levels of visualization for a gene query; foremost is the expression across hematopoietic cell types, second is analysis of survival of Acute Myeloid Leukaemia patients based on gene expression, and lastly, the expression visualized in an interactive developmental tree. With the introduction of single cell data we have now also included an unbiased dimensionality reduction method to show gene expression over the continuum of haematopoiesis. The webserver includes a few select analysis functionalities, like Student's t-test, identification of correlating genes and lookup of whole genetic signatures, with the aim of making generation and testing of hypotheses quick and intuitive. The visualizations have been updated to accommodate new datatypes and the database has been largely expanded with RNA-sequencing datasets, both purified in bulk and at single cell resolution, increasing the number of single samples more than 10 fold, while keeping simplicity in presentation. The database should be of interest for any researcher within leukaemia, haematopoiesis, cellular development, or stem cells. The database is freely available at www.bloodspot.eu.
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- Authors
- Bagger, F. O., Kinalis, S., & Rapin, N.
- Affiliations
- University of Copenhagen (DK)
- Corresponding author
- Bagger, Frederik Otzen
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-11-05
- Volume
- 47
- Issue
- D1
- Pages
- D881-D885
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6323996
- OpenAlex
- W2900119089
- Cited by
- 229
- References
- 27
- Citations by year
- 2026: 7 · 2025: 22 · 2024: 40 · 2023: 41 · 2022: 39 · 2021: 34 · 2020: 36 · 2019: 10
- FWCI
- 14.33
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, cc-by-nc)
- Funders
- Lundbeck Foundation (R193-2015-1611, R182-2014-3881)
- Novo Nordisk Foundation (NNF15CC0027852)
- Topics
- Health Sciences › Medicine › Hematology › Acute Myeloid Leukemia Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- hematopoiesis, gene expression database, single-cell RNA sequencing, acute myeloid leukemia, patient survival, dimensionality reduction, gene expression signatures, leukemia, stem cells
- MeSH terms
- RNA-Seq, Cell Separation, Flow Cytometry, Hematopoiesis, Hematopoietic Stem Cells, Humans, Leukemia, RNA, Messenger, Databases, Genetic, Single-Cell Analysis
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