30k Mouse E18 Combined Cortex, Hippocampus and Subventricular Zone Nuclei Multiplexed, 12 CMOs

Nuclei were isolated from four E18 mouse combined cortex, hippocampus and ventricular zone tissues (C57BL/6 strain), obtained by 10x Genomics from BrainBits LLC. The four E18 mouse nuclei samples were multiplexed at equal proportions with 3 CMOs per nuclei sample, resulting in a pooled sample labeled with 12 CMOs. Nuclei from the non-multiplexed sample were used as one of the four sample types composing the multiplexed sample.

The config.csv input file was submitted with four sample IDs (correlating to the four E18 mouse nuclei samples) and with three respective CMO IDs assigned per sample ID.

The sample was run with intron mode. Libraries generated from neuronal nuclei typically have higher levels of reads mapped antisense to genes.

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: 28,017 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: 31,171
• Cells Assigned to a Sample: 23,900

Individual Multiplexed Samples - Key Metrics