| Antibodies |
| CD64 |
Biolegend |
Cat# 139307, RRID:AB_2561962 |
| Mertk |
Thermo Fisher |
Cat# 12–5751–82, RRID:AB_257262 |
| SiglecF |
BD Bioscience |
Cat# 564514, RRID:AB_2738833 |
| Bacterial and Virus Strains |
| M.tuberculosis Erdman mCherry |
Originally from Tanya Parish lab https://dx.plos.org/10.1371/journal.pone.0009823
|
N/A |
| Critical Commercial Assays |
| Ribo-Zero Gold rRNA Removal Kit (Epidemiology) |
Illumina |
Cat# MRZE724 |
| Glycoblue |
Thermo Fisher |
Cat# AM9515 |
| Seahorse XFp Cell Mito Stress Test Kit |
Agilent |
Cat# 103010–100 |
| Deposited Data |
| Bystander AM and IM populations |
GEO: GSE108844
|
N/A |
| MicroArray studies |
Rohde et al., 2012; Schnappinger et al., 2003
|
N/A |
| Experimental Models: Organisms/Strains |
| C57BL/6J mice |
The Jackson Laboratory |
Cat# JAX:000664, RRID:IMSR_JAX:000664 |
| Software and Algorithms |
| DESeq2 |
Love et al., 2014 |
N/A |
| ApeGLM |
Zhu et al., 2019 |
N/A |
| GSEA |
Broad Institute http://software.broadinstitute.org/gsea/index.jsp
|
N/A |
| EnrichmentMap |
Reimand et al., 2019 |
N/A |
| FastQC (v. 0.11.5) |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
N/A |
| Flexbar (v. 3.4) |
Roehr et al., 2017 |
N/A |
| Bowtie2 |
Langmead and Salzberg, 2012 |
N/A |
| Hisat2 (v. 2.1.0) |
Kim et al., 2015 |
N/A |
| HTSeq (v. 0.11.0) |
Anders et al., 2015 |
N/A |
