For isolated nuclei 25,000 reads each are recommended, For most applications, an average of 40,000 reads per cell should be sequenced (for cell types with complex transcriptomes).(The assay requires at least a 28 cycle forward read, a 10 bp dual index reads, and a 90 cycle reverse read). The 10X GEX Single-Cell libraries are most economically sequenced on the Illumina NovaSeq 6000 with paired-end reads. Compatible with Illumina and Element Biosciences Aviti sequencers.Recovers up to ~65% of cells (typically 50%).Captures 100-20,000+ cells per sample and up to 320,000 cells (or ~ 1 million cells with multiplexing) per run in ~20 minutes.Fast workflow from cell suspension to 3′-cDNA or 5′-cDNA library.The principles of the 10X Single-Cell RNA-seq library preparation: In addition, the Bioinformatics Core has developed a custom single-cell data analysis pipeline for 10X data.
#10X CHROMIUM DROPLET BASED FREE#
The resulting data can be analyzed with the free Cell Ranger and Loupe Cell Browser software.
Up to sixteen samples can be processed per batch within minutes. The single-cell encapsulating process is significantly faster compared to other technologies. In contrast to other protocols, the 10X controller can load “all” droplets with micro-beads, enabling single-Poisson distribution loading and thus high capture efficiencies (in contrast to double-Poisson loading of other protocols). (These numbers can be further increased with sample multiplexing.) Each bead is loaded with adapters containing one of 750,000 different barcodes for the single cell RNA-seq library preps. The 10X Genomics Single Cell suite enables high capture efficiency (of up to 65% of cells loaded) with a flexible workflow, encapsulating 500 to 20,000 cells or nuclei per library together with micro-beads into nano-droplets. Due to ongoing COVID19 testing, we have suspended customer instrument use temporarily. This is advantageous if your group is planning a large number of single-cell experiments. UC Davis users with BSL1 samples can access our 10X Chromium controller as part of our shared instruments for customer use. We can also connect you with your local 10X sales specialists and scientists for office hour appointments! We offer free joint consultations with the Bioinformatics core.
Make sure you discuss and plan your experiment with us several weeks in advance and to schedule your cell drop-offs without staff.
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