Bulk RNA-seq of macrophages isolated from Salmonella Typhimurium infected zebrafish embryos

Bacterial infection involves a complex interaction between the pathogen and host where the outcome of infection is not solely determined by pathogen eradication. To identify small molecules that promote host survival by altering the host-pathogen dynamic, we conducted an in vivo chemical screen using zebrafish embryos and found that treatment with 3-hydroxy-kynurenine protects from lethal gram-negative bacterial infection. 3-hydroxy-kynurenine, a metabolite produced through host tryptophan metabolism, has no direct antibacterial activity but enhances host survival by restricting bacterial expansion in macrophages by targeting kainate-sensitive glutamate receptors. These findings reveal new mechanisms by which tryptophan metabolism and kainate-sensitive glutamate receptors function and interact to modulate immunity, with significant implications for the coordination between the immune and nervous systems in pathological conditions., The transcriptomes of macrophages isolated from zebrafish embryos (3 dpf) were analyzed by RNA sequencing. Briefly, fluorescently labeled cells were isolated in bulk from a single cell suspension obtained by enzymatic digestion of groups consisting of 5 homozygous Tg(mpeg1:mCherry) transgenic animals (8-11 biological replicates/condition) following the protocol as described in the flow cytometry section. cDNA libraries were constructed from a range of 50-800 collected cells with an in-house adaptation of the Smart-seq2 protocol in combination with the Nextera XT Library preparation kit (Illumina, Inc., San Diego, CA). Library size and concentration were evaluated using the TapeStation 2200 system (Agilent) and a Qubit fluorometer (Invitrogen) before sequencing. Samples were multiplexed and paired-end sequences of 50 bp were generated on a NovaSeq S4 6000 sequencing system (Illumina) generating on average 1.03e8 reads per sample. Samples were demultiplexed and FASTQ files representing ea..., , # Bulk RNA-seq of macrophages isolated from Salmonella Typhimurium infected zebrafish embryos

From the article: A tryptophan metabolite modulates the host response to bacterial infection via kainate receptors

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## Data Descriptions

The following macrophages bulk RNA-seq dataset files are available

1. Count Matrix (parada_et_al_2023_counts.csv): table with genes in rows and samples in columns.
2. Metadata (parada_et_al_2023_metadata.csv): table with Sample N°, Sample Name, experimental condition, and exp_date (experimental date) information.
3. Raw RNAseq Data in fastq.gz: 118 files corresponding to read 1 (R1) and read 2 (R2) from pair-end sequencing of 59 samples.

Experimental conditions:

* *uninfected*: macrophages isolated from control uninfected, untreated animals
* *uninfected_3hk*: macrophages isolated from uninfected and 3hk treated animals
* *exposed*: macrophages not containing bacteria isolated from salmonella infected animals
* *exposed_3hk*: macrophages n...