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.

A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.

“…The available samples were put into groups based on relevant study variables and genes were ranked according to the different groups comparisons. A detailed description of the GXB software tool is available from recent publications 19– 21 . This software interface allows user to easily navigate and filter the dataset collection.…”

“…The identified datasets are particularly relevant to our interest in understanding the pathobiology of VRTI and vaccination. As described in recent publications 18, 19 , these datasets were loaded into a custom interactive web application, the Gene Expression Browser (GXB), which enables easy access to large datasets and interactive visualization of our dataset collection related to VRTI and vaccination against respiratory viruses. It also provides access to demographic and clinical information.…”

Using ‘collective omics data’ for biomedical research training

“…The dataset collections described in papers published by Sidra scientists covered a wide range of sometimes very narrowly focused subject matters, including: human monocyte immune biology, development and differentiation of placenta, functional programming of haematopoietic cells in early life, embryonic development in healthy individuals and patients with polycystic ovary syndrome, human immunobiology of human immunodeficiency virus infection and breast cancer immune classification …”

“…A proof of principle was recently obtained with one trainee completing all three modules . Five other scientists having completed at least one training module …”

A curated transcriptome dataset collection to investigate inborn errors of immunity

“…A web tutorial for the use of GXB can be accessed at:https://gxb.benaroyaresearch.org/dm3/tutorials.gsp#gxbtut. A detailed description of GXB has been recently published[19][20][21][22] and is reproduced here so that readers can use this article as a standalone resource. Briefly, datasets of interest can be quickly identified either by filtering on criteria from pre-defined sections on the left or by entering a query term in the search boxat the top of the dataset navigation page.…”