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Welcome to SBR-Blood for Mus musculus

SBR-Blood is a database, or more imaginative a data ranch, where data are curated/cultivated, repositories grown and analyses harvested. SBR-Blood contains next-generation sequencing and array-based data for different cell types in the hematopoietic stem-cell differentiation process. The management system associated with the boutique provides capabilities for the analysis (in particular union and intersection correlations) of single and multiple cell types as well as branches of the hematopoietic stem cell differentiation tree.

Abstract

Extensive research in hematopoiesis (formation and maturation of blood cells) over several decades has provided much information and generated large datasets of expression (via arrays and RNA-seq) and several epigenetic features (via methyl-seq and ChIP-seq) in multiple blood cell types in human as well as mouse. However, no coherent explanatory model has emerged for how gene regulatory processes lead to the different mature blood cell types. Further progress depends on effective integration among the diverse datasets. Current databases are limited, in that some focus only on microarray expression data (e.g. BloodExpress and EpoDB) while others host generic experimental data (e.g. NCBI GEO), and few provide methodologies to compare different experimental datasets on the fly. To bring together diverse datatypes and allow for user-initiated analyses, we have developed a new database framework, called SBR-Blood.

The SBR-Blood data ranch presented here offers access to both array-based mRNA expression profile data and high-throughput sequencing data from hematopoietic cells along with the methodologies for correlative and integrative analyses. The database organizes information by the identity of specific cell types (e.g. hematopoietic stem cells) or paths in the differentiation process (e.g. erythropoiesis, the process that generates red blood cells) defined via cell surface markers. Metadata include the method used to generate the data and the associated publication. Each cell type or path in the differentiation process can be intersected or combined with others to generate gene and peak lists that can be mined for functional or regulatory information.

The current version of SBR-Blood is populated with data about hematopoiesis in the mouse (Mus musculus) and contains publicly available microarray mRNA expression data as well as sequence-based data for mRNA levels, methylation, histone modifications and transcription factor occupancy. The validity and usability of SBR-Blood has been established through the reproduction of workflows applied in the analysis of previously published studies.

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