GSM9098124: Dual-species_ST_replicate2_day2_day4_MRSA_mouse_kidney_infection; Staphylococcus aureus; Mus musculus; OTHER
FFPE tissue sections were cut at 5 µm thickness and mounted on Visium Spatial slides (Visium V5 Slide FFPE v2) according to the protocol CG000408. Deparaffinization, H&E staining, and decrosslinking were performed following the User Guide CG000409. Library construction was done at the Indiana University Center for Medical Genomics Core following the Visium CytAssist Spatial Gene Expression for FFPE Reagent Kits User Guide (CG000495). During the probe hybridization step, we compared the effects of MRSA cell wall permeabilization using either the default Enzyme B (included in the Visium FFPE Reagent Kit, cat. no. 1000362) or achromopeptidase (Sigma A3547; working concentration 5 U/mL) on consecutive slides. The overall MRSA read counts were comparable between the two permeabilization methods. The custom probes were prepared as a combined spike-in pool (LHS and RHS) at a concentration of 24 nM per probe as described in the 10X technical note CG000621. cDNA libraries were then prepared and sequenced on an Illumina NovaSeq 6000.