RNA-sequencing of neonatal monocyte responses to E. coli and S. epidermidis

Newborns, particularly those born prematurely, are extremely vulnerable to sepsis and this has been attributed to 'immature' innate monocyte defences. Predominant pathogens include Escherichia. coli and Staphylococcus. epidermidis but no studies have assessed global transcriptional responses of neonatal monocytes to live sepsis-causing bacteria. Here, we aimed to identify and characterise the common and pathogen-specific, neonatal monocyte transcriptional responses to E. coli and S. epidermidis to better understand early life innate immune responses. RNA-sequencing was performed on purified cord blood monocytes from very preterm (<32 weeks gestational age, GA) and term infants (37-40 weeks GA) following standardised challenge with live S. epidermidis or E. coli. Overall design: 43 samples in total from 4 term infants, 5 preterm infants exposed to chorioamnionitis and 6 preterm infants without exposure to chorioamnionitis. Each individual has an unstimulated monocyte sample, and a E. coli- or S. epidermidis-stimulated monocyte sample (3 samples per individual) except for two individuals (preterm infants without exposure to chorioamnionitis) which only have an unstimulated monocyte sample and one of either E. coli- or S. epidermidis-stimulated mnocytes.