scRNA-seq of mouse lymph node stromal cells

C57BL/6 mouse lymph node stromal cells were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3' Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip. 5-10 x 104 reads/cell were obtained with characterization of 2-3 x 103 transcripts/cell. Overall design: After enzymatic digestion of the lymph nodes (LNs)from C57BL/6 mice, CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells. For scRNA-seq, more than 2x104 CD45- LN stromal cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells into nanoliter-scale droplets containing uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3' Reagent Kit (v3 chemistry) (10x Genomics, Pleasanton, CA). Generated cDNA libraries were sequenced on a NovaSeq 6000 sequencing system. 4 x 103 cells per sample were captured on the 10X Chromium chip, 5-10 x 104 reads/cell were obtained with a characterization of 2-3 x 103 transcripts/cell.