Chromium microfluidic system

For single-cell experiments, 14 cell vials from different individuals (7 male and 7 female) were snap-thawed in a 37 o C water bath and serially diluted in RPMI 1640 medium (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich) medium. Cells were counted and equal cell numbers per individual were pooled in two pools of 7 individuals each. Cell pools were concentrated and resuspended in PBS supplemented with 0.04 % bovine serum albumin, and loaded separately or as a combined pool with cells of all 14 individuals on the Chromium microfluidic system (10X Genomics) aiming for 8,000 or 25,000 cells per run. Single cell libraries were generated using the Chromium Single Cell 3′library and gel bead kit v2 (PN #120237) from 10X Genomics. The cells were sequenced with a targeted depth of approximately 50,000 reads per cell on the HiSeq4000 (Illumina) with 150 bp paired-end sequencing of read2 (exact numbers for each run in Supplementary Table S2).

For single-cell experiments, 14 cell vials from different individuals (7 male and 7 female) were snap-thawed in a 37 o C water bath and serially diluted in RPMI 1640 medium (Sigma-Aldrich) supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich) medium. Cells were counted and equal cell numbers per individual were pooled in two pools of 7 individuals each. Cell pools were concentrated and resuspended in PBS supplemented with 0.04 % bovine serum albumin, and loaded separately or as a combined pool with cells of all 14 individuals on the Chromium microfluidic system (10X Genomics) aiming for 8,000 or 25,000 cells per run. Single cell libraries were generated using the Chromium Single Cell 3′library and gel bead kit v2 (PN #120237) from 10X Genomics. The cells were sequenced with a targeted depth of approximately 50,000 reads per cell on the HiSeq4000 (Illumina) with 150 bp paired-end sequencing of read2 (exact numbers for each run in Additional file 1: Table S1).