241009_feature_counts.csv

Bone marrow-derived macrophages (BMDMs) were generated by harvesting cells from the bone marrow of PTPN2 wild-type (WT), heterozygous (HET) and knockout (KO) mice, and growing them<i> ex vivo</i>. They were differentiated into macrophages by stimulating them with 30 ng/mL recombinant murine M-CSF for 7 days. BMDMs were either maintained as naive macrophages (M0) or polarized towards the M1 pro-inflammatory phenotype with IFN-ɣ and lipopolysaccharide (LPS), or towards the M2 anti-inflammatory phenotype using IL-4 for 24 hours. Macrophages were then harvested from the plates and counted for downstream experiments.RNA from purified BMDMs was isolated with TRIzol and samples were subjected to RNA-sequencing (RNA-Seq) using an Illumina HiSeq 2500. Transcript abundances were quantified with Kallisto v0.41.1 using paired-end reads pseudo-aligned to the mouse transcriptome (GENCODE M17). Differential gene expression analysis was performed by importing Kallisto results with tximport v1.6.0, followed by DESeq2 v1.18.1. InnateDB and gene ontology (GO) were used for downstream analysis to identify pathways and biological processes enriched in specific populations.