Titles and Legends to Figures
Supplementary Table 1
A table shows all 752 genes selected for the macrophage signatures. Descriptions for
columns are:
A) Probe ID: Log2 ratio stripcharts of probes are attached as comments and are visible
when mousing over the probe IDs in the Excel format.
B) Signature: Probes are classified according to expression profiles.
C) Mouse Gene ID: Probes are mapped to mouse Entrez Genes. Gene IDs are
hyperlinked to NCBI Entrez Gene. Empty gene ID indicates that no Entrez Gene was
found.
D) Mouse Symbol: The “Official Symbol” for the mouse Entrez Gene is listed. Some
genes are listed with two common symbols. For probes with no Entrez Genes, their gene
symbols are EST names prefixed with “EST”. ESTs or genes without predicted proteins
are labeled with “no CDS”. Probes mapped to introns of genes are labeled with “intron”.
E) Mouse Description: The “Gene description” of the mouse Entrez Gene is listed.
F) Human Gene: Mouse genes are mapped to Entrez human orthologs. Gene IDs are
hyperlinked to NCBI gene sites. An empty gene ID indicates that no human Entrez Gene
was found.
G) Human Symbol: The “Official Symbol” for the human Entrez Gene is listed.
H) Human Description: The “Gene description” of the human Entrez Gene is listed.
I) Genentech ID: Genentech gene ID.
J) Gene Family: Genes are assigned to gene families as in Table 1.
K) Chromosome: The chromosome location of the above mouse gene is shown. Genes
mapped to X and Y chromosomes are removed.
The values below are used to select genes and are described in Materials and Methods.
L) Mean Fold Change
M) Gap Fold Change
N) Gap Range
O) Gap Comparison
P) T test p-value
Q) F test p-value
R-AI) Expression values (log2 ratio): Empty values indicate that expression levels cannot
be determined or are unreliable.
Supplementary Table 2
Gene Ontology assignments of 752 genes with the highest degree of statistical
significance measured by the p-value of the chi-square test show functions associated
with macrophage biology and the immune system (647 of the genes have a GO
assignment).
Supplementary Table 3
Cell surface receptors with less well known macrophage functions than those genes listed
in Table 2 also show different expression patterns across macrophage cell types.
Supplementary Table 4
A table of pair-wise Pearson correlation values between samples based on the log2
expression ratio shows sample correlation. High correlation coefficients between
biological replicates are highlighted in green, and those correlation coefficients outside of
biological replicates are highlighted in blue.
Supplementary Figure 1
Flow cytometry analysis, purity assessment, and expression levels of cell surface markers
confirm the identity of the purified macrophages. A, B, C and D) Flow cytometry plots
represent cell populations of the indicated enriched cells. The purified cells are labeled as
Kwt, Kko, P+, P-, Sneg and Slow on the plots, and cell purity of greater than 95% was
confirmed by FACS analysis. E, F and G) Agilent expression values (log2 ratio) of
F4/80, CRIg and Cd11b are consistent with the protein levels detected by flow cytometry
shown in A, B, C and D.
Supplementary Figure 2
The Bioanalyzer shows high quality of RNA samples obtained from sorted macrophages.
Supplementary Figure 3
TaqMan qPCR confirms microarray results. The fold changes of expression levels of
Cd163, Stab1 and Pf4 between Kwt and Kko, P+ and P- detected by microarray and
TaqMan are shown in A an B respectively. Error bars represent the standard error of the
mean (SEM) for quadruplicate (qPCR) or triplicate (microarray) samples.
Supplementary Figure 4
Schematic of macrophage gene signature selection as described in Materials and
Methods.