Abstract
During haematopoiesis, haematopoietic stem cells differentiate into restricted potential progenitors before maturing into the many lineages required for oxygen transport, wound healing and immune response. We have updated Haemopedia, a database of gene-expression profiles from a broad spectrum of haematopoietic cells, to include RNA-seq gene-expression data from both mice and humans. The Haemopedia RNA-seq data set covers a wide range of lineages and progenitors, with 57 mouse blood cell types (flow sorted populations from healthy mice) and 12 human blood cell types. This data set has been made accessible for exploration and analysis, to researchers and clinicians with limited bioinformatics experience, on our online portal Haemosphere: https://www.haemosphere.org. Haemosphere also includes nine other publicly available high-quality data sets relevant to haematopoiesis. We have added the ability to compare gene expression across data sets and species by curating data sets with shared lineage designations or to view expression gene vs gene, with all plots available for download by the user.
Highlights
Haematopoiesis is the process that forms the cells of the blood; haematopoietic cells range from stem cells that are capable of self renewal and of reconstituting all other haematopoietic lineages, to the many mature cells that fight infection, carry oxygen and clot the blood
We have previously published a comprehensive database of microarray gene expression profiles from FACS sorted samples of wildtype mouse haematopoietic cell types, Haemopedia [1], with associated analysis and data visualisation tools on www.haemosphere.org, which has been a useful and popular resource for researchers working in haematopoiesis and cellular differentiation
Our platform allows the integration of additional RNA-seq samples as they become available, to provide an even more comprehensive insight into geneexpression during haematopoiesis
Summary
Haematopoiesis is the process that forms the cells of the blood; haematopoietic cells range from stem cells that are capable of self renewal and of reconstituting all other haematopoietic lineages, to the many mature cells that fight infection, carry oxygen and clot the blood. In order to compare genes across species and data sets, we have manually curated the cell types in each data set with a common set of lineage annotations We have used this to produce a multi-species plot, where the expression pattern of a gene can be compared between mouse and human (Figure 2), or more generally between data sets, which allows cross-platform comparison between the RNAseq and microarray data sets. A table of differentially expressed genes is returned with the log fold change and adjusted P value This table can be downloaded for further analyses, viewed as a heatmap across all cell types in the data set for the top 300 genes or mapped to the mouse or human orthologues. To guide users through the major functions of the database, we have included tours of main pages which can be accessed by clicking on the ‘?’ symbol on the pages
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