Cells from four E18 mouse combined cortex, hippocampus and ventricular zone tissues (C57BL/6 strain) were obtained by 10x Genomics from BrainBits LLC. Cells from the four E18 mouse tissues were multiplexed at equal proportions with 3 CMOs per tissue, resulting in a pooled sample labeled with 12 CMOs. Cells from the non-multiplexed sample were used as one of the four sample types that composed the multiplexed sample.
The config.csv input file was submitted with four sample IDs (correlating to the four E18 mouse tissues) and with three respective CMO IDs assigned per sample ID.
Libraries were prepared following the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing User Guide (CG000388) and sequenced on Illumina NovaSeq 6000.
Single Cell 3’ Cell Multiplexing v3.1 Dual Index Library
- Sequencing Depth: 25,417 read pairs per cell
- Paired-end, dual indexing Read 1: 28 cycles (16 bp barcode, 12 bp UMI); i5 index: 10 cycles (sample index); i7 index: 10 cycles (sample index); Read 2: 90 cycles (transcript)
Pooled Multiplexed Sample - Key Metrics
- Estimated Number of Cells: 33,197
- Cells Assigned to a Sample: 23,338
Individual Multiplexed Samples - Key Metrics
| Metric | Brain 1 | Brain 2 | Brain 3 | Brain 4 |
|---|---|---|---|---|
| Cells Assigned to a Sample | 5,642 | 6,075 | 5,802 | 5,819 |
| Median Genes per Cell | 2,484 | 2,400 | 2,406 | 2,516 |
| Median UMI Counts per Cell | 5,769 | 5,462 | 5,487 | 5,869 |