Spleen. See the “Sample processing for scRNA-seq” section.

Lymph nodes. Mice were euthanized with isoflurane overdose, and lymph nodes were harvested from inguinal, mesenteric, cervical, and axillar areas. Then, lymph nodes were mashed into a 70-μm cell strainer, and cells were washed and counted.

Blood. Blood was collected into EDTA-coated tubes (MiniCollect, Greiner Bio-One) from euthanized mice using cardiac puncture. Red blood cells were then lysed using blood lysis buffer (BD Biosciences), and the remaining leukocytes were washed twice and counted.

Bone marrow. Mice were euthanized with isoflurane overdose. Femurs and tibias were collected. Cells from the BM were obtained by flushing the bones with injected sterile PBS. Red blood cells were removed using 500 μl of (ACK) lysis buffer for 1.5 min.

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