A HaemAtlas: characterizing gene expression in differentiated human blood cells
Hematopoiesis is a carefully controlled process that is regulated by complex networks of transcription factors that are, in part, controlled by signals resulting from ligand binding to cell-surface receptors. To further understand hematopoiesis, we have compared gene expression profiles of human erythroblasts, megakaryocytes, B cells, cytotoxic and helper T cells, natural killer cells, granulocytes, and monocytes using whole genome microarrays. A bioinformatics analysis of these data was performed focusing on transcription factors, immunoglobulin superfamily members, and lineage-specific transcripts. We observed that the numbers of lineage-specific genes varies by 2 orders of magnitude, ranging from 5 for cytotoxic T cells to 878 for granulocytes. In addition, we have identified novel coexpression patterns for key transcription factors involved in hematopoiesis (eg, GATA3-GFI1 and GATA2-KLF1). This study represents the most comprehensive analysis of gene expression in hematopoietic cells to date and has identified genes that play key roles in lineage commitment and cell function. The data, which are freely accessible, will be invaluable for future studies on hematopoiesis and the role of specific genes and will also aid the understanding of the recent genome-wide association studies.
Keywords
Hematopoiesis; Cell-surface receptors; Gene expressionData / Code
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - Expression patterns of known transcription factors in haematopoietic cell lineages
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- 158kB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - A summary of samples used to generate the HaemAtlas data, including information on cell and RNA purity
description - application/ms-excel
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- 21kB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - Full blood counts plus C-reactive protein and Erythrocyte sedimentation rate data for all volunteers used in the study
description - application/ms-excel
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- 14kB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - ZLists of present genes for each of the eight cell types in the study
description - application/ms-excel
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- 9MB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - Probes considered differentially expressed (DE) in the study. A file is present for each cell as reference. Probes are indicated by 1 if they were upregulated and −1 if they were downregulated in the test cell relative to the reference
description - application/ms-excel
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- 12MB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - Lists of lineage specific genes for each of the eight cell types in the study. Illumina probe IDs (the sequences of which are given) have been mapped to Ensembl Gene, Transcript and Protein IDs. External Gene IDs are also given where available.
description - application/ms-excel
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- 477kB
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subject - Data
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- Available under Creative Commons: Attribution-Noncommercial 3.0
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info - Monoclonal antibodies and fluorochromes used for flow cytometric analysis of T cell subsets
description - application/ms-excel
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- 13kB
