RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer's instructions 1.1 μl of purified macrophage RNA (6 ng/ μl) from each sample was added to a well of a 384-well PCR plate (Greiner, 785290) containing 20 nM of an air dried indexed polydT primer (custom made, IDT). Minibulk transcriptome libraries were generated using a modified CEL-Seq2 protocol (Hashimshony et al., 2016, Genome Biol.) with the following adaptations: first strand cDNA synthesis was performed, then the samples were treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) in a final reaction volume of 20 ul and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.