Massively parallel digital transcriptional profiling of single cells. NGS Lab, GX, Terry JM, Belgrader P, et al. If you are interested in using this technology in your research, please do not hesitate to contact us. Recommended coverage (Cells): 50 000 reads per cell.
10x chromium gem software#
Other software packages for downstream analysis such as Supernova for de-novo assembly, Cell Ranger for transcriptomics or Loupe for visualization are also freely available. Each droplet contains several molecules and thus it gives the capacity of reconstructing 5 – 10 million of 50 kb molecules or to analyze several hundred thousands of individual cells. It is very important to point out that the GemCode technology leverages existing short-read sequencers (Illumina, see below) and is easily integrated into existing laboratory workflows.įor reconstruction of source molecules The Long Ranger open-source software is being used. The Chromium controller is using 750,000 different barcodes. Library construction using GEM is performed using Chromium controller instrument which might be best described as a hybrid between a flow cytometer and an emulsion PCR machine. In case of DNA, primers also include a part of P5 adaptor and in case of RNA, the UMI part (Unique Molecular Identifier) which might be used to reduce the quantitative bias introduced by replication. Primers used for extension, at first attached to the surface of a gel bead, contain the annealing part, 14 bases long barcode and Illumina read one primer specific sequence.
10x chromium gem full#
These molecules are not extended to its full length but only to the length compatible with Illumina sequencers. In droplets, long molecules (DNA or RNA) are amplified using primer extension. Long molecules capture (left) and Cells capture (right) These fragments when sequenced are used for reconstruction of its source molecule (DNA) or for analyzing transcriptome of each single cell (RNA). The GEM technology (Gel bead in Emulsion) enables to capture long DNA molecules or RNA from single cells into droplets where they are turned into droplet-specific (or source molecule/cell-specific) barcoded short fragments. Sub-population classification revealed by single cell transcriptomics.True haplotype assembly with linked reads.Deletion revealed by phasing linked reads.SNPs relationship revealed by phasing linked reads.In the picture below you can see some application examples (Zheng et al. Cell sorting in population based on actual expression.View into genome regions inaccessible to short-range sequencer.Reconstruction of up to several tens of Mb long haplotype blocks.Long range information from short reads.The key highlights of the Chromium system are: The GemCode technology has been developed by the 10xGenomics company, based in Pleasanton, California and is being represented by an innovative system that transforms short-read sequencing technologies - Chromium System. In this post, we are happy to announce its availability to our clients and provide its basic description. Our constant search for the best and most appropriate solutions to various experimental designs has led us to the introduction of the GemCode technology into our portfolio of Next-Generation sequencing services.
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