Chromium System Brochure

Introducing the Chromium™ System
One system, one workflow, powerful
new sequencing applications
10xGenomics.com
10x Genomics
Changing the Definition of Sequencing™
The Chromium™ System
One system, one workflow, powerful
new sequencing applications
GemCode™ technology powers an innovative system that transforms the
capability of existing short-read sequencers. With millions of uniquely
addressable partitions, the Chromium System unlocks critical
genomic information.
Genome Sequencing
Targeted Sequencing
The Chromium Genome provides long range
information on a genome-wide scale, including
variant calling, phasing and extensive
characterization of genomic structure. Unlock
critical genetic information for variants in heritable
disorders, and discover key alterations in cancer.
The Chromium Exome provides long range
information, enabling phasing, structural variant
detection and copy number determination. Low
complexity and repetitive regions previously missed
with short-read sequencing are now accessible.
Single Cell Sequencing
De Novo Assembly
With Chromium Single Cell 3’, perform deep profiling
of complex cell populations with high-throughput
digital gene expression on a cell-by-cell basis. Trace
expression profiles to individual cells to ensure
biologically relevant signals are not masked by bulk
average measurements.
Discover the true genome with the Supernova™
Assembler and open the door to low-cost,
everyday diploid assemblies. Unlock samplespecific sequence, probe diploid genome
structure, and remove the need for a reference
sequence of any kind.
The Chromium™ System
Unlock critical long range
genomic and cell-by-cell gene
expression information.
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10x Genomics
Changing the Definition of Sequencing™
Chromium™ Genome
The most comprehensive genome
Long range genomes at population scale. Call and phase the full spectrum of
variants and unlock previously inaccessible regions from a single library.
Resolve the genome into multi-megabase phase blocks
While human genomes are diploid, analysis based on short reads collapses variants into a single haploid call
set, masking critical genetic relationships. Chromium Genome phases the full spectrum of variants (SNVs,
indels, and large-scale structural rearrangements) into ultra long multi-megabase phase blocks, enabling a full
understanding of diploid genome sequence.
50 Mb Phase Block
Chr 6
Massive partitioning and complete genomic information from a single library with 1ng input
The Chromium Genome performs massive partitioning and barcoding of 1ng input DNA. The system produces uniform,
high-complexity libraries, compatible with Illumina’s HiSeq X Ten systems, enabling high quality variant calling from
minimal sequencing depth.
Hap 1
STANDARD
BARCODING
Chromium
Genome
Partitions
384
>1,000,000
Barcode Pool
384
4,000,000
100ng+
1ng
Input DNA
™
Hap 2
70 kb Deletion
Uncover previously inaccessible parts of the genome and hidden variants in critical genes
Multi-megabase diploid assemblies eliminate the need for a reference
Short reads cannot be mapped into repetitive regions, causing regions with no coverage (Child: BWA Aligner).
The Lariat™ Aligner uses Linked-Read information to map reads that could not normally be mapped (Child Lariat Aligner),
enabling variant calling and phasing in regions normally inaccessible to short reads. Father: NA12891 Child: NA12878
Mother: NA12892.
The Supernova™ Assembler utilizes Linked-Reads to de novo construct multi-megabase diploid assemblies,
preserving phasing information for small variants, structural rearrangements and novel sequence.
Chr15
RPS17 Exon 3
Father
Lariat Aligner
Child
Lariat Aligner
Mother
Lariat Aligner
Child
BWA Aligner
G
G
G
A
G
Child
G
A
A
G
G
C
Mother
A
A
G
G
C
G
Father
3
MAPQ>30
A
Detection of a SNP in
RPS17. The Lariat Aligner
uses barcode information
to correctly map reads
and call variants in a
highly repetitive region that
standard aligners miss due
to low mapping quality.
A region in chromosome 3 is
represented in the diploid assembly
of NA12878 by two >10Mb phased
scaffolds within a larger 17Mb overall
scaffold segment. A zoom into the
figure shows that variants between
the haplotypes are conserved
in the assembly such as the 8kb
deletion indicated, where traditional
assemblies compress the two
haplotypes into a single path.
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10x Genomics
Changing the Definition of Sequencing™
Chromium™ Exome
In collaboration with
Reach beyond the exome
The Chromium Exome with optimized baits powered by Agilent’s marketleading SureSelect® technology enables access to low complexity and
duplicated regions, megabase-scale phasing, structural and copy number
variation while improving the quality of SNP calls.
Resolve compound heterozygosity and copy number change
Establish cis or trans relationships between variants without trio sequencing.
TRPV1
SHPK
CTNS
P2RX5-TAX1BP3
Coverage
G>A
Hap1
57kb Deletion
Enable phasing of thousands of genes and detection of structural and copy number variation
The optimized SureSelect baits are designed specifically for the Chromium Exome to improve gene phasing
by closing gaps, and recovering hard-to-map loci in the genome.
Hap2
Exome Baits
Linked-Reads from
Exome Baits
Identify structural variants
Detect gene fusions, duplications, deletions and translocations from a single exome run.
Optimized
SureSelect Baits
13 Mb
EML4
Linked-Reads from
Chromium Exome
ALK
Coverage
BC
Overlap
Map previously inaccessible regions and improve variant calling performance
The barcode-aware Lariat™ Aligner maps reads in previously inaccessible regions, identifies
new variants and eliminates false positives due to incorrect mapping.
Linked
Reads
7,693 bp
RPS17
Optimized
SureSelect Baits
NA12878
Lariat Aligner
NA12878
BWA Aligner
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MAPQ>30
5
6
20
29
EML4-ALK
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10x Genomics
Changing the Definition of Sequencing™
Chromium™ Single Cell 3’
High-throughput single cell
RNA sequencing
Profiling 1,000s to 10,000s
of cells per experiment
increases sensitivity and
accuracy for the detection
of rare cell types.
Single cell resolution is the key to uncovering the true complexity of
heterogeneous populations. Chromium Single Cell 3’ provides scalable
transcriptional profiling of 1,000s to 10,000s of individual cells.
Efficient biochemistry captures thousands
of genes per cell
Differential expression identifies cell cycle phase
Number of distinct genes detected per cell as a function of sequencing
coverage for HEK293T cells. Graph shows mean (black line) and range
(dark gray) over 16 independent experiments.
Proliferating HEK293T cells were profiled and scored for expression
of markers associated with each major cell cycle phase. Cells from all
phases were identified at expected proportions.
Single cell partitioning with low multiplet rates
Mouse transcript counts
60,000
Human:Mouse
Human only
Mouse only
0
Human transcript counts
60,000
Approximately 1,400 human (HEK293T) and mouse (NIH3T3) cells were
mixed at a 1:1 ratio prior to profiling. 99.4% of the resulting cell-containing
GEMs gave rise to sequencing reads mapping to only one species. This
implies a total doublet rate of 1.0%.
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High-throughput
Up to 8 channels processed in parallel
1,000 to 6,000+ cells per channel
10 minute run time per chip
No cell size restrictions
~50% cell processing efficiency
t-SNE projection of gene expression profiles from 68,000 unsorted
human peripheral blood mononuclear cells (PBMCs). Colors indicate the
closest match in a reference panel of sorted cell types.
Multiple key applications
Immunology
Neurobiology
Cancer Biology
Stem Cell Research
Embryology
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10x Genomics
Changing the Definition of Sequencing™
Make the Discovery with GemCode™ Technology
GemCode Technology with millions
of uniquely addressable partitions
enables single molecule resolution
and single cell sequencing
GemCode™ Technology Process
™
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Gel bead
Disposable
microfluidics
Definitive results
Mega diversity reagent libraries.
Highly automated reaction
assembly.
Single cell analysis on a
massive scale.
Up to 100 million barcoded oligos
per bead.
Millions of “effective” pipette
steps per minute.
Creating
the GEMs
Functionalized with defined DNA
barcodes.
Deformable polymeric beads
dissolve on demand.
Droplet
Monodisperse water-in-oil
droplets.
Implementing
the GEMs
Discovering
with GEMs
Single molecule resolution.
On a single instrument
Touch screen operation.
~10 minute run time.
Massively scalable
to millions of partitions.
Together make a GEM
Gelbead in Emulsion.
Uniquely addressable reactions
for molecular barcoding on a
massive scale.
>90% of all droplet reactions
receive a single barcoded
gel bead.
Gel bead in emulsion (GEM)
Barcode and reagent delivery
with sample partitioning on a
massive scale.
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10x Genomics
Changing the Definition of Sequencing™
Partitioning & Molecular Barcoding at Scale
Partition sample across 100,000s
to 1,000,000s of partitions, each
containing a unique barcode
DNA
Linked-Reads
Barcoded Fragment
Embedded Barcode
Genome is replicated and barcoded via a low-level enzymatic replication.
Enzyme
GEMs
Collect
Pool
Lines represent Linked-Reads. Dots represent reads.
Color indicates barcode. Reads with same barcode originated
from molecules encapsulated in the same partition.
Barcoded Primer Library
DNA or Cells
Gel beads loaded with barcoded
oligonucleotides are first mixed
with sample and enzyme mixture,
then combined with an oilsurfactant solution at a microfluidic
‘double-cross’ junction.
Oil
Gel bead-containing droplets (GEMs) flow to
a reservoir and are harvested. Gel beads are
dissolved and molecular barcoding of the sample
is initiated. The barcoded products are pooled
from each droplet. Standard library construction
adds the remaining sequencing adapters and
sample indices.
Single Cell
Digital Gene
Expression
Barcoded cDNA
Cell
Cell
Embedded Barcode
Cell
Cell
mRNA is transcribed by a reverse transcriptase that
creates barcoded cDNA.
Cell 1...
Cell 5,000
Gene 1
Gene 2...
Gene 2,000
Gene 1
Gene 2...
Gene 2,000
A barcode identifies transcripts originating from a single cell,
which are then counted.
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10x Genomics
Changing the Definition of Sequencing™
The Chromium™ Software Suite
Linking data, developers and discovery
Long Range Genomes and Exomes
Single Cell Transcriptomics
Long Ranger Analysis Pipelines
Cell Ranger™ Analysis Pipelines
Leverage molecular barcoding to generate a
powerful data type called Linked-Reads. Novel
algorithms in the Long Ranger pipelines yield several
classes of biological insights from Linked-Reads:
Turn-key analysis for single cell gene expression
sequencing data. Combining robust transcriptome
alignment with large scale cellular barcoding, the
Cell Ranger pipelines rapidly generate expression
profiles to shed light on:
™
•Barcode-aware alignment
•Megabase-scale haplotype phasing
•Structural variant detection and phasing
•Greater accuracy in SNP and indel calling
•Complex primary cell populations
•Cellular heterogeneity in cancer tumors
•Cell cycle behavior
Building upon widely accepted aligners and variant callers such as
BWA, GATK, and Freebayes, the Long Ranger pipelines leverage the
Chromium System’s molecular barcoding to enable phasing and
structural variant calling.
De Novo Assembly
Open Source Informatics
Supernova Assembler
Martian™ Technology
The Chromium System opens the door to low-cost,
everyday diploid genome assemblies. The Supernova
Assembler leverages the unique properties of
Linked-Read data to reconstruct the genome under
study, without the need for a reference genome.
Chromium Software is built using a powerful, open
source informatics platform called Martian. The
Martian language features an elegant syntax for
defining complex pipelines. A lightweight runtime
featuring a micro-container design is performanceoptimized for high-throughput NGS analysis, and
includes powerful data management features.
™
The Supernova Assembler exploits Linked-Read data to reconstruct a
diploid genome, unlocking sample-specific sequence and removing the
need for a reference sequence of any kind.
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Starting with pre-built or user-supplied transcriptomes, the Cell Ranger
pipelines can process cellular barcodes to produce gene expression
profiles across tens of thousands of cells at once.
The Martian language is complemented by a type-checking compiler,
visual IDE, and debugging and profiling tools. The Martian runtime
provides built-in support for pipeline composability, parallelization, and
parameter sweeping.
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10x Genomics
Changing the Definition of Sequencing™
The Loupe haplotype view displays multi-megabase phase blocks and structural variant calls. Above, an
example of compound heterozygosity is shown where the variants involved are fully contained within large,
contiguous phase blocks.
The Loupe™ family of visualization applications
brings clarity to the novel biological insights made
possible by the Chromium System.
The Loupe structural variant view lists the
calls and candidates produced by the Long
Ranger pipelines, and uses changes and gaps
in color intensity to represent barcode-based
evidence of structural rearrangements.
For genomes and exomes: fully haplotype-enabled genome browsing
and structural variant visualization. For single cell transcriptomics:
dimensionality reduction, clustering, and isolation of cell types
and phases.
Loupe applications feature fluid, modern user interfaces, run on
Windows and Mac, and work with files produced by the Long Ranger
and Cell Ranger pipelines.
The Loupe single cell analysis view features an array of techniques for dimensionality reduction and clustering
which can be applied to gain insight into a variety of single cell experiment types.
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10x Genomics
10x Genomics, Inc.
About us
10x Genomics meets the critical need for long range, structural and cellular
information, with an innovative system that transforms the capability of existing
short-read sequencers. Our Chromium™ System supports comprehensive
genomics and high-throughput single cell transcriptomics. It enables
researchers to discover previously inaccessible genomic information at
unprecedented scale, including phased structural variants, phased single
nucleotide variants, and dynamic gene expression of individual cells—while
leveraging their existing sequencing systems and workflows.
10xGenomics.com
Contact Us
Pleasanton, CA
10x Genomics, Inc.
7068 Koll Center Parkway,
Suite 401
Pleasanton, CA 94566
17
+1 925 401 7300
+1 800 709 1208
[email protected]
San Francisco, CA
10x Genomics, Inc.
160 Spear Street,
Suite 1130
San Francisco, CA 94105
+1 925 401 7300
+1 800 709 1208
[email protected]
© 2016 10x Genomics, Inc. All rights reserved. Duplication and/or reproduction of all or any portion of this document without the express written consent
of 10x Genomics, Inc., is strictly forbidden. Nothing contained herein shall constitute any warranty, express or implied, as to the performance of any
products described herein. Any and all warranties applicable to any products are set forth in the applicable terms and conditions of sale accompanying
the purchase of such product. 10x Genomics provides no warranty and hereby disclaims any and all warranties as to the use of any third party products
or protocols described herein. The use of products described herein is subject to certain restrictions as set forth in the applicable terms and conditions
of sale accompanying the purchase of such product. “10x”, “10x Genomics”, “Changing the Definition of Sequencing”, “Chromium”, “GemCode”, “Loupe”,
“Long Ranger”, “Cell Ranger”, “Lariat” and “Supernova” are trademarks of 10x Genomics, Inc. All other trademarks are the property of their respective
owners. All products and services described herein are intended FOR RESEARCH USE ONLY and NOT FOR USE IN DIAGNOSTIC PROCEDURES.
Changing the Definition of Sequencing™
10xGenomics.com