KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Streptococcus pneumoniae: serotype 4 | Laboratory strain, gifted by | N/A |
| strain: TIGR4 | Dr. Elaine Tuomanen | |
| Streptococcus pneumoniae: serotype 4 | Laboratory strain, gifted by | N/A |
| strain: TIGR4 | Dr. Timothy van Opijnen | |
| Streptococcus pneumoniae: serotype 23 strain: DAW7 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV2 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV3 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV4 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV5 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV8 | Clinical isolate, this paper | N/A |
| Group viridans streptococcus: SV11 | Clinical isolate, this paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4R1P.1 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4R2P.1 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4R2P.2 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4R3P.1 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4R3P.2 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP1 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP2 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP3 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP4 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP5 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP6 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP7 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4EP8 | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: N132P | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: N232P | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: N332P | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: N432P | This paper | N/A |
| Streptococcus pneumoniae: serotype 4 strain: T4trDAW7 | This paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| BOCILLIN™ FL Penicillin, Sodium Salt | Invitrogen | Cat# B13233 |
| Pfizerpen® penicillin G potassium | Pfizer, requested from St. Jude Pharmacy | CAS: 113-98-4 |
| Neomycin | Sigma | Cat# N6386; CAS: 1405-10-3 |
| Defibrinated Sheep’s Blood | Lampire | Cat# 103-100-3 |
| Triton X-100 | Sigma | Cat# X100; CAS: 9036-19-5 |
| Complete, EDTA-free protease inhibitor cocktail tablets | Roche | Cat# 11-836-170 |
| NuPAGE™ LDS Sample Buffer (4X) | ThermoFisher Scientific | Cat# NP0007 |
| TNF-α | ThermoFisher Scientific | Cat# 554618 |
| F12K | ThermoFisher Scientific | Cat# 21127022 |
| Fetal Bovine Serum | Atlanta Biologicals | Cat# S11150 |
| Gentamicin sulfate | Sigma | Cat# G1914 |
| Trypsin-EDTA | ThermoFisher Scientific | Cat# 15400054 |
| Penicillin-Streptomycin (10,000 U/mL) | ThermoFisher Scientific | Cat# 15140122 |
| DMEM | ATCC | Cat# 30-2002 |
| BSA | Sigma | Cat# A9418 |
| Proteinase K | Sigma | Cat# P4850 |
| Phenol:Chloroform:isoamyl alcohol | Sigma | Cat# 77617 |
| Chloroform:isoamyl alcohol | Sigma | Cat# C0549 |
| Penicillin E-test strips | Liofilchem | Cat# 921030 |
| p-chloro-phenylalanine | Cayman | Cat# 26168 |
| ExTaq HS Polymerase | Takara | Cat# RR006B |
| erythromycin | Sigma | Cat# E5389 |
| Critical commercial assays | ||
| Milliplex® MAP Kit | EMD Millipore | Cat# MCYTOMAG-70K |
| Nextera XT DNA Library Prep Kit | Illumina | Cat# FC-131-1096 |
| Deposited data | ||
| Pneumococcal genome sequence data | This paper | SRA: PRJNA737504, BioSample: SAMN29540204 |
| Experimental models: Cell lines | ||
| Human: A549 lung epithelial cells | ATCC | CCL-185 |
| Mouse: J774A.1 macrophages | ATCC | TIB-67 |
| Experimental models: Organisms/strains | ||
| Mouse: BALB/c | The Jackson Laboratory | RRID: IMSR_JAX:000651 |
| Oligonucleotides | ||
| Primers for barcoded pneumococcal strains, see Table S2 | This paper | N/A |
| Software and algorithms | ||
| Trim Galore version 0.6.4 | Babraham Bioinformatics | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| breseq version 0.35.5 | Deatherage et al.48 | https://github.com/barricklab/breseq/releases |
| bowtie2 version 2.3.5 | Langmead et al.49 | https://github.com/BenLangmead/bowtie2/releases |