Publications

Macrophages

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J.
Nat Microbiol. 2016 Nov 14;2:16206. 
DOI : https://www.nature.com/articles/nmicrobiol2016206 
PMID: https://pubmed.ncbi.nlm.nih.gov/27841856/ 
Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79363

Fibroblast-IL-7 feedback drives PDPN+ monocytes to restrain CD4+ T cell responses. 
Fu Y, Toussaint C, Sauerland I, Reiss E, Philipsen L, Gintschel P, Knop L, Braun A, Kruse B, Dewitz LA, Amore J, Dovhan V, Weinert S, Jantz-Naeem N, Baars I, Mohr J, Prein J, Schwendele C, Bruno P, Boettcher M, Groeger N, Van Hove H, Greter M, Becher B, Kahlfuss S, Schraven B, Geffers R, Tueting T, Joller N, Fricke S, Saliba AE, Schueler T, Mueller AJ
BioRxiv 2026.03.24.713728
DOI: https://doi.org/10.64898/2026.03.24.713728 
Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228455 

Single-bacteria RNA-seq

Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium.
Bornet E, Witzky A, Riedel T, Dersch P, Bohn E, Westermann AJ.
Cell Rep. 2025 Jun 24;44(6):115844.
DOI: https://doi.org/10.1016/j.celrep.2025.115844 
PMID: https://pubmed.ncbi.nlm.nih.gov/40526469/ 
Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE289312

Transcriptomic profiling of individual bacteria by MATQ-seq.
Homberger C, Imdahl F, Hayward RJ, Barquist L, Saliba AE, Vogel J.
Nat Protoc. 2025 Apr 9.
DOI: https://doi.org/10.1038/s41596-025-01157-5 
PMID: https://pubmed.ncbi.nlm.nih.gov/40204970/ 
Data: https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA904727

A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria.
Homberger C, Saliba AE, Vogel J.
Methods Mol Biol. 2023;2584:105–121.
DOI: https://doi.org/10.1007/978-1-0716-2756-3_4 
PMID: https://pubmed.ncbi.nlm.nih.gov/36495446/

Improved bacterial single-cell RNA-seq through automated MATQ-seq and Cas9-based removal of rRNA reads.
Homberger C, Hayward RJ, Barquist L, Vogel J.
mBio. 2023 Apr 25;14(2):e03557-22.
DOI: https://doi.org/10.1128/mbio.03557-22 
PMID: https://pubmed.ncbi.nlm.nih.gov/36880749/ 
Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE218633

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria
Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J. 
Nat Microbiol. 2020 Oct;5(10):1202-1206.
DOI: https://doi.org/10.1038/s41564-020-0774-1 
PMID: https://pubmed.ncbi.nlm.nih.gov/32807892/ 
Data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119888