ORCID Profile
0000-0002-7287-1636
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Publisher: F1000 Research Ltd
Date: 30-03-2016
DOI: 10.12688/F1000RESEARCH.8375.1
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 s le 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 s les. 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: m3/geneBrowser/list .
Publisher: F1000 Research Ltd
Date: 02-11-2018
DOI: 10.12688/F1000RESEARCH.16622.1
Abstract: Monitoring of blood transcriptional changes during disease or treatment could improve the understanding of cellular mechanisms associated with that particular condition. This can be achieved through serial s ling of small blood volumes. However, molecular analysis of gene expression from low volume s les remains a challenging task. To address this issue, we have developed a set of standard operating procedures (SOP), starting from collection of small volume blood to measurement of gene expression. Previously we published an SOP for the collection of a small volume of blood via finger stick and stabilization of RNA. The aim of this manuscript is to share a modified Tempus TM solution based RNA extraction method, developed in our lab, for the extraction of total RNA from low volume whole blood s les collected via finger stick.
No related grants have been discovered for Basirudeen Syed Ahamed Kabeer.