Spreadsheet: ba84e482-86cd-421e-ae7d-4839e52dc591
Sheet: Sheet1

Table S2: Summary of individual experiments in the infection time-series data compendium analyzed | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7
Experiment name | Cell type | Organism | Strain | Time points (hrs) | Reference | Comments
m0 [NAME] | macrophage (primary) | none |  | 1, 6, 12, 24 | Nau2002
[NAME] | macrophage (primary) | none |  | 0.5, 1, 6, 12, 24 | Nau2002
m0 control3 | macrophage (primary) | none |  | 1, 2, 6, 12, 24 | Nau2002
m0 control4 | macrophage (primary) | none |  | 1, 2, 6, 12, 24 | Nau2002
m0 Latex | macrophage (primary) | none |  | 1, 6, 12, 24 | Nau2002
m0 E. coli | macrophage (primary) | Escherichia coli | sd-4 | 0.5, 1, 6, 12, 24 | Nau2002
m0 EHEC | macrophage (primary) | Escherichia coli | EHEC O157:H7 | 1, 2, 6, 12, 24 | Nau2002
m0 S. typhi | macrophage (primary) | Salmonella typhi | Quailes | 1, 2, 6, 12, 24 | Nau2002
[NAME] | macrophage (primary) | Salmonella typhimurium |  | 1, 2, 6, 12, 24 | Nau2002
m0 S. aureus | macrophage (primary) | Staphylococcus aureus | ISP794 | 1, 2, 6, 12, 24 | Nau2002
m0 L. monocytogenes | macrophage (primary) | [NAME] monocytogenes | EGD | 1, 2, 6, 12, 24 | Nau2002
m0 M. tuberculosis | macrophage (primary) | Mycobacterium tuberculosis | Erdman | 0.5, 1, 6, 12, 24 | Nau2002
m0 M. bovis BCG | macrophage (primary) | Mycobacterium bovis | BCG | 1, 6, 12, 24 | Nau2002
m0 LPS E | macrophage (primary) | Escherichia coli |  | 1, 2, 6, 12, 24 | Nau2002 | LPS from E. coli
m0 LPS S | macrophage (primary) | Salmonella |  | 1, 2, 6, 12, 24 | Nau2002 | LPS from Salmonella
m0 LTA | macrophage (primary) | Staphylococcus aureus |  | 1, 2, 6, 12, 24 | Nau2002 | Lipoteichoic acid
m0 MDP | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2002 | Muramyl dipeptide
m0 TB hsp70 | macrophage (primary) | Mycobacterium tuberculosis |  | 1, 2, 6, 12, 24 | Nau2002 | recombinant source
m0 BCG hsp65 | macrophage (primary) | Mycobacterium bovis | BCG | 1, 2, 6, 12, 24 | Nau2002 | recombinant source
m0 MPA | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2002 | [NAME] lipid A (detoxified lipid A)
m0 f-MLP | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2002 | formyl-methionine-leucine-phenylalanine
m0 Protein A | macrophage (primary) | Staphylococcus aureus |  | 1, 2, 6, 12, 24 | Nau2002 | Protein A
m0 Mannose | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2002 | D-(+)-mannose
m0 IFN-alpha | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2003
m0 IFN-beta | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2003
m0 IFN-gamma | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2003
m0 IL-10 | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2003
m0 IL-12 | macrophage (primary) |  |  | 1, 2, 6, 12, 24 | Nau2003
m0 (U937) [NAME] | macrophage (cell line) |  |  | 0.5, 1, 2, 4, 6 | Boldrick2002
m0 (U937) B. pertussis 338 | macrophage (cell line) | Bordetella pertussis | Bp338 | 0.5, 1, 2, 4, 6 | Boldrick2002
m0 (U937) B. pertussis 537 (avirulent) | macrophage (cell line) | Bordetella pertussis | [NAME] (avirulent) | 0.5, 1, 2, 4, 6 | Boldrick2002 | lacks many virulence factors, including adenylate cyclase and pertussis toxin
m0 (U937) B. pertussis A2-6 (AC-) | macrophage (cell line) | Bordetella pertussis | BpA2-6 (lacks adenylate cyclase toxin) | 0.5, 1, 2, 4, 6 | Boldrick2002
m0 (U937) B. pertussis Tox6 (PT-) | macrophage (cell line) | Bordetella pertussis | BpTox6 (lacks pertussis toxin) | 0.5, 1, 2, 4, 6 | Boldrick2002
DC control1 | dendritic cell (primary) | none |  | 1, 2, 4, 8, 12, 18, 24 | Huang2001
[NAME] | dendritic cell (primary) | none |  | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001
DC control3 | dendritic cell (primary) | none |  | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001
DC E. coli | dendritic cell (primary) | Escherichia coli | SD54 | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001
DC Influenza | dendritic cell (primary) | Influenza virus | A/PR/8/34 | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001
DC C. albicans | dendritic cell (primary) | Candida albicans | HLC54 | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001
DC LPS | dendritic cell (primary) | Escherichia coli | 055:B5 | 1, 2, 4, 8, 12, 18, 24, 36 | Huang2001 | LPS from E. coli
DC PolyIC | dendritic cell (primary) |  |  | 1, 2, 4, 8, 12, 18, 24 | Huang2001 | poly I:C (synthetic dsRNA)
DC Mannan | dendritic cell (primary) | Saccharomyces cerevisiae |  | 1, 2, 4, 8, 12, 18, 24 | Huang2001 | yeast cell-wall component
PBMC control1 | peripheral blood monocytes (primary) |  |  | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002
PBMC B. pertussis LPS | peripheral blood monocytes (primary) | Bordetella pertussis |  | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002
PBMC B. pertussis 338 | peripheral blood monocytes (primary) | Bordetella pertussis | Bp338 | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | live organism
PBMC B. pertussis Minnesota1 | peripheral blood monocytes (primary) | Bordetella pertussis | Heat-killed Minnesota isolate | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | heat killed; Minnesota is a virulent strain
PBMC E. coli | peripheral blood monocytes (primary) | Escherichia coli | Heat-killed | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | clinical isolate
PBMC S. aureus (1) | peripheral blood monocytes (primary) | Staphylococcus aureus | Heat-killed isolate 1 | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | clinical isolate
PBMC S. aureus (2) | peripheral blood monocytes (primary) | Staphylococcus aureus | Heat-killed isolate 2 | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | clinical isolate
PBMC Ionomycin+PMA | peripheral blood monocytes (primary) |  |  | 0.5, 1, 2, 4, 6, 12, 24 | Boldrick2002 | mimics antigen stimulation
PBMC B. pertussis 338 Killed | peripheral blood monocytes (primary) | Bordetella pertussis | Bp338 heat-killed | 0.5, 2, 4, 6, 12 | Boldrick2002 | from another donor
PBMC B. pertussis 338 Live | peripheral blood monocytes (primary) | Bordetella pertussis | Bp338 live | 0.5, 2, 4, 6, 12 | Boldrick2002 | from another donor
WB control NP | whole blood (primary) | none |  | 1, 3, 6, 12, 24 | Pathan2004 | blood from healthy donor NP
WB control SW | whole blood (primary) | none |  | 1, 3, 6, 12, 24 | Pathan2004 | blood from healthy donor SW
[NAME] meningitidis NP | whole blood (primary) | Neisseria meningitidis | Serogroup B, type MC58 | 1, 3, 6, 12, 24 | Pathan2004
[NAME] SW | whole blood (primary) | Neisseria meningitidis | Serogroup B, type MC58 | 1, 3, 6, 12, 24 | Pathan2004
Epithelial cell control | Gastric epithelial (cell line) | none |  | 1, 3, 6, 12, 24 | Guillemin2002
Epithelial cell H. pylori G27 | Gastric epithelial (cell line) | Helicobacter pylori | G27 | 1, 3, 6, 12, 24 | Guillemin2002 | wild-type
Epithelial cell H. pylori cagN- | Gastric epithelial (cell line) | Helicobacter pylori | cagN- | 1, 3, 6, 12, 24 | Guillemin2002 | protein encoded by the pathogenicity island
Epithelial cell H. pylori cagA- | Gastric epithelial (cell line) | Helicobacter pylori | cagA- | 1, 3, 6, 12, 24 | Guillemin2002 | cagA is injected into the host cell via a type IV secretion system and leads to host cell elongation
Epithelial cell H. pylori cagE- | Gastric epithelial (cell line) | Helicobacter pylori | cagE- | 1, 3, 6, 12, 24 | Guillemin2002 | apparently triggers NFKB activation and IL8 synthesis
Epithelial cell H. pylori PAI- | Gastric epithelial (cell line) | Helicobacter pylori | PAI- | 1, 3, 6, 12, 24 | Guillemin2002 | the entire pathogenicity island (encodes all the above and other proteins)