10X Genomics has developed a highly multiplexed micro-droplet reagent delivery system that, when combined with a short read sequencing platform, provides long range genome information that enables phasing and structural variation analysis. The latest version of this platform, the Chromium™ System, is an updated version of the awkwardly named “GemCode Technology Platform”. Its one million partitions enable whole genome sequencing (using data from Illumina’s HiSeq X platform), exome sequencing, and even single cell RNA-Seq.
- $125k system price
- 1M partitions
- 4M barcodes
The GemCode technology works by taking gel beads loaded with barcoded oligos and mixing them with sample and an enzyme mixture. Individual beads are captured as a droplet (GEM) in an oil emulsion. The GEMs are then pooled, the beads are dissolved, and the DNA (as few as five molecules per GEM when one sample is spread across one million GEM partitions) is amplified and tagged with the barcoded oligo. The barcoded DNA is then used to prepare a standard Illumina sequencing library (although in principle it could be used with any sequencing short read sequencing platform). The GemCode technology adds $450 to the cost of whole genome sequencing and $250 to the cost of exome sequencing.
In addition to generating linked reads for long range genomic applications, the Chromium System can also be used for single cell RNA-Seq applications. Instead of barcoding amplified DNA fragments from the same genomic region, all transcripts from individual cells get barcoded with the same index sequence. This allows for the transcripts from several thousand individual cells to be pooled together in a single sequencing run. The GemCode technology adds up to $1.20 per cell to the cost of creating a transcriptome profile.
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