title: A curated transcriptome dataset collection to investigate the functional programming of human hematopoietic cells in early life.
abstract: Compendia of large-scale datasets made available in public repositories provide an opportunity to identify and fill gaps in biomedical knowledge. But first, these data need to be made readily accessible to research investigators for interpretation. Here we make available a collection of transcriptome datasets to investigate the functional programming of human hematopoietic cells in early life. Thirty two datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application called the Gene Expression Browser (GXB), which was designed for interactive query and visualization of integrated large-scale data. Quality control checks were performed. Multiple sample groupings and gene rank lists were created allowing users to reveal age-related differences in transcriptome profiles, changes in the gene expression of neonatal hematopoietic cells to a variety of immune stimulators and modulators, as well as during cell differentiation. Available demographic, clinical, and cell phenotypic information can be overlaid with the gene expression data and used to sort samples. Web links to customized graphical views can be generated and subsequently inserted in manuscripts to report novel findings. GXB also enables browsing of a single gene across projects, thereby providing new perspectives on age- and developmental stage-specific expression of a given gene across the human hematopoietic system. This dataset collection is available at: http://developmentalimmunology.gxbsidra.org/dm3/geneBrowser/list.
authors.affiliation: Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Mahbuba
authors.initials: M
authors.lastname: Rahman
authors.affiliation: Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Sabri
authors.initials: S
authors.lastname: Boughorbel
authors.affiliation: Benaroya Research Institute, Seattle, WA, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Presnell
authors.affiliation: Benaroya Research Institute, Seattle, WA, USA.
authors.forename: Charlie
authors.initials: C
authors.lastname: Quinn
authors.affiliation: Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Chiara
authors.initials: C
authors.lastname: Cugno
authors.affiliation: Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Damien
authors.initials: D
authors.lastname: Chaussabel
authors.affiliation: Sidra Medical and Research Center, Doha, Qatar.
authors.forename: Nico
authors.initials: N
authors.lastname: Marr
keywords: B cells;; PBMC; T cells; Tregs; fetal; hematopoietic cells; immune ontogeny; peripheral blood; transcriptomics; umbilical cord blood