GSM7157619: E13.5, scRNAseq TotalSeq2 [MP]; Mus musculus; RNA-Seq
Cells from each condition were resuspended in 90μl FACS buffer (PBS without Ca2+ or Mg2+ with 10% FCS), stained with barcode tagged antibodies against MHCII (B0117), CD40 (B0903), CD80 (B0849), with biotinylated UEA1 bound to SAV-PE-B0952) and with a-EPCAM-magnetic beads (Miltenyi) (see Supplementary Table 3), and washed.  Each condition was then hashed with 100ullipid anchoredCell Multiplexing Oligosfor sample multiplexing (CMOs, 10x Genomics). Cells eluted from the column were spun down and resuspended in 50µlFACS buffer, of which 10µlwas taken for cell counting.Approximately a total of 15000-30000 cells pooled from each condition were then filtered and loaded on a Chip G (10X Genomics). Cell-bead encapsulation was performed running the chip in a Chromium X instrument (10X Genomics). Upon encapsulation, gene expression and multiplexing libraries were prepared following the manufacturer's instructions using the Chromium Next GEM single cell reagent kit 3' V3.1 (dual index) with Feature Barcoding technology for Cell Multiplexing (CG000388, 10x Genomics). Libraries were quantified using a Bioanalyzer DNA High-sensitivity Kit (Agilent Technologies), pooled at a molar ratio of 6:1 between gene expression and multiplexing libraries, and sequenced on an Illumina NextSeq 2000 P3 flow cell (100 cycles configuration) to obtain approximately 1.4B paired-end reads.