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10X Genomics Chromium System Technology

The Chromium system is based on the GemCode technology which is composed of millions of unique emulsions containing a single high molecular weight DNA molecule or a single cell. Each emulsion or partition has its own unique barcode.

Two types of libraries are available for three types of applications:

  • Single Cell 3' for transcriptomic studies
  • DNA libraries for linked reads (genome phasing and identification of structural variants) and de novo assembly of large genomes.

Single Cell 3'

The Chromium single cell protocol allows single cell quantification of RNA transcripts from a population of various cell types. There is a separate barcode for discriminating each sample, each cell and also every independent transcript.

Libraries generated are sequenced on HiSeq2500 or 4000 instruments in paired-end formats for reads lengths of 50, 75 or 100 bases.

Sequences can be downloaded directly from Nanuq and include 10X tags.

Data can be analyzed directly using Cell Ranger and Loupe Cell Browser, free tools available from 10X Genomics: (link).

DNA libraries

Chromium Genome protocol provides long-range information on a genome-wide scale, enabling de novo genome assembly and also variant calling, phasing and extensive characterization of genomic structure.

A unique barcode is added per emulsion to tag a single long fragment (60-100kb). The generated libraries can be sequenced on the HiSeq X instrument in paired-end format for read lengths of 150 bases.

Sequences with embedded 10X tags can be downloaded directly from Nanuq.

The data can be directly used with 10X tools such as Long Ranger and Supernova (link).

For more information, contact the Client Management Office.