Immunological Genome Project Data Analysis

Immunological Genome Project (ImmGen) raw expression data of phase 1 and 2 were downloaded as CEL files from GEO (GSE15907 and GSE37448), processed and normalized using the Robust Multi-array Average (RMA) procedure on probe-level data using Matlab functions. The analysis was performed using custom CDF file obtained from Brainarray^{50 (link)}. Blueprint and Encode data were processed as we described previously^{51 (link)}. Raw counts from the lung reference dataset were obtained from Gibbings et al.^{27 (link)} (GSE94135) and Altboum et al.^{26 (link)} (GSE49932). Counts were normalized and converted to TPM using R functions. Gene expression profile of GM-CSF derived bone marrow dendritic cell subsets (available at GSE62361¹⁸) was analyzed using the GEO2R tool for differentially expressed genes. Top 50 upregulated by fold-change of GM-DCs genes and top 50 GM-Macs were used in Figure 1b. Single-cell RNA-seq counts from Hashimshony et al.^{15 (link)} used in Figure 1b were downloaded from the ARCHS project^{52 (link)}. 10X PBMC single-cell counts were downloaded directly from the 10X website (https://support.10xgenomics.com/single-cell-gene-expression/datasets ).