Processed macrophage sequencing data
Processed macrophage sequencing data. Samples include human alveolar macrophages (AMs), tumor-associated macrophages from lung tumors (TAMs), and differentially polarized human monocyte-derived macrophages (MDMs) as detailed in Hoppstädter et al., 2021 (DOI: https://doi.org/10.1016/j.ebiom.2021.103578). Raw data were deposited in the Gene Expression Omnibus (GEO) database (GEO datasets GSE162669 and GSE162698). Gene expression clustering was done with hierarchical clustering in R. genes were screened for the enrichment of transcription factor binding using the iRegulon software. Raw counts (TPM) are listed in TMP_all_samples_with_symbols. Genes within clusters are listed in Clusters_GeneIDs, and enrichment of transcription factor binding sites within clusters are given in Clusters_ResultsiRegulon. For GO term analysis see Clusters_Go_Enrichment.
Steps to reproduce
AMs/TAMs: AMs and TAMs were obtained from isolated from human lung tumor tissue or the autogenic non-tumor lung tissue obtained from patients undergoing lung resection as previously described (Hoppstädter et al., Front Pharmacol, 2015; doi:10.3389/fphar.2015.00055). Samples from three donors were analyzed in triplicate. MDMs were generated as described previously (Dembek et al., Immunobiology, 2017; doi:10.1016/j.imbio.2017.01.003). After differentiation in M-CSF-containing medium for 6 d, MDMs were polarized for another 24 h. MDM medium was supplemented with 20 ng/ml IFNγ and 100 ng/ml LPS for M1 polarization; either 20 ng/ml IL4 or IL10 for M2 polarization; or left without further supplementation for M0 macrophages. TAM-like macrophages were generated by cultivation in A549-tumor cell-conditioned medium. Samples from three donors were analyzed. Further details are given in Hoppstädter et al., 2021 (DOI: 10.1016/j.ebiom.2021.103578).