Fig. 1

Sample processing overview. Thirty newborns were recruited in The Gambia, with each newborn providing a peripheral blood sample on DOL0 and subsets of ten newborns each providing a second peripheral blood sample at either DOL1, 3 or 7, resulting in a total of 60 blood samples. Newborn peripheral venous blood was drawn directly into heparinized collection tubes. Aliquots (200 μl) were removed for transcriptomic analysis. Plasma was then harvested from the remaining whole blood after a spin, and cryopreserved for cytokine, proteomic and metabolomic analyses. The remaining cellular fraction was diluted with phosphate-buffered saline (PBS) to replace the volume of plasma removed, and 100 μl aliquots from this mixture were processed for single-cell immunophenotyping by flow cytometry. With a starting volume of 1 ml, this standard operating protocol still left the cellular fraction contained in 400 µl of starting blood volume that could be used for other analyses. DOL: day of life