Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

<p><strong>Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of <em>Ms4a3</em>^Ai14 at onset and peak EAE using 10X Genomics platform.</strong></p> <p>The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer&#39;s protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell.</p> <p>Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from <em>Ms4a3</em>^Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger&#39;s in-built cell calling algorithms, we proceeded with Seurat v4 workflow.</p>