Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell...

37
Illumina ® | Bio-Rad ® Single Cell Sequencing For Research Use Only. Not for use in diagnostic procedures.

Transcript of Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell...

Page 1: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

© 2016 Illumina, Inc. All rights reserved.Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, ForenSeq, Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect, MiniSeq, MiSeq, MiSeqDx, MiSeq FGx, NeoPrep, NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome, TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the US and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.

Illumina® | Bio-Rad®

Single Cell Sequencing

For Research Use Only. Not for use in diagnostic procedures.

Page 2: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

2

Macosko et al, Cell: May, 2-15

44k single cells – 39 retinal cell types

“The single cell ‘omics revolution is firmly underway. Nearly every expression study worth doing will be worth doing at single cell level…” Ewan Birney, EMBL

The importance of single cell sequencing

For Research Use Only. Not for use in diagnostic procedures.

Page 3: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

3

Single-cell analysis – a brief history

Kolodziejczyk, et. al. 2015; Navin, 2015

Single cell qPCR of neurons,

Eberwine, et.al.

First single-cell mRNA sequenced, Tang, et.al.

STRT-Seq5’ end Seq

Islam, et. al.

SMART-Seq2Increased sensitivity

Picelli, et.al.

CEL-SeqRemove PCR bias

with IVTHashimshony, et. al.

SMART-SeqFull length pre-amp

Ramskold, et. al.

SC whole transcriptome microarrays

DNA-Seq of single human cancer cell, Navin, et.al.

Incorporation of UMI’s to methods

Jaitin, et. al.Islam, et. al.

Drop-SeqMacosko, et. al.

Single cell WGS of

Neurons, Evrony, et.al.

First single-cell exome sequenced,

Xu, et.al.

First single-cell T-cell

epigenome with HiC,

Nagano, et.al.

MALBACZong, et.al.

SC RNA-Seq of immune

cells, Shalek, et.al.

Organ lineage tracing with

SC RNA-Seq, Truetlein, et.al.

SC ATAC-Seq of human cell lines, Cusanovich, et.al.

Page 4: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

4

Single-Cell Sequencing

0

50

100

150

200

250

300

1990 1995 2000 2005 2010 2015

Pap

ers

Pubmed: "Single-cell Sequencing"

2013

Page 5: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

5

Why Perform Single Cell Analysis ?

1. Assess cell-to-cell heterogeneity

4. Infer gene regulatory networks

2. Map cell trajectories

3. Dissect transcriptional

mechanics

Page 6: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

6

Assessing Heterogeneity in Cancer

Tirosh et al., 2016, Science

Page 7: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

7

Illumina® | Bio-Rad®

Single Cell Transcriptome Sequencing Solution

For Research Use Only. Not for use in diagnostic procedures.

Page 8: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

8

The Illumina | Bio-RadSingle Cell Sequencing Solution

ddSEQ Single-Cell Isolator

SureCell WTA 3’ Library Prep Kit Single Cell RNA Seq v1.0.0

NextSeq, HiSeq, NovaSeq

For Research Use Only. Not for use in diagnostic procedures.

Page 9: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

9

Single Cell Isolation Principle

Single-Cell Suspension

Cell Isolation Reagents (including barcodes)

Isolate thousands of cells in minutes

Oil

Oil

ddSEQ™ Single-Cell Isolatorwith Droplet Digital™ Technology

Single-Use Microfluidic Cartridges

For Research Use Only. Not for use in diagnostic procedures.

Page 10: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

10

Single Cell Isolation Principle

Single-Cell Suspension

Cell Isolation Reagents (including barcodes)

Isolate thousands of cells in minutes

Oil

Oil

ddSEQ™ Single-Cell Isolatorwith Droplet Digital™ Technology

Single-Use Microfluidic Cartridges

For Research Use Only. Not for use in diagnostic procedures.

Page 11: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

11

Experimental Design for the ddSEQ™ System

For Research Use Only. Not for use in diagnostic procedures.

Oil

Oil

Microspheres

Cells

1 Cartridge:• 4 wells with samples• Load 4.5ul of cell suspension per well• 2,500 cells/ul• 11,250 cells loaded per well• Collect 300-375 cell+bead droplets per sample

Goal = 1 cell & 1 bead

Cell+Bead capture rate 3-4%

Page 12: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

12

Cell Preparation Methods

Solid tissue dissociation

Tissue culture

Trypsinize, Wash& Filter (35um strainer)

FACS

S3e™ Cell Sorter

Clump-free Single Cell suspension

Page 13: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

13

Quality Assessment and Cell Counting

● Cells must be free of clumps to prevent multiple cells per droplet

● Suspension concentration must be accurately determined

● Free of debris from dead or damaged cells- Trypan blue staining

ZOE™ Cell Imager

TC20™ AutomatedCell Counter

Page 14: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

14

SureCell™ WTA 3’ Library Preparation

● Single cell encapsulation with the ddSEQ™ Single-Cell Isolator

Microspheres

Cells

For Research Use Only. Not for use in diagnostic procedures.

TTTTT

UMICell BarcodeRead1

TTTTT

TTTTT

Page 15: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

15

SureCell™ WTA 3’ Library Preparation

● Single cell encapsulation with the ddSEQ™ Single-Cell Isolator

● Modified Nextera®

Library prep

● Sensitive assay chemistry without pre-amplification

Microspheres

Cells

For Research Use Only. Not for use in diagnostic procedures.

● First strand synthesis in droplets

Page 16: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

17 For Research Use Only. Not for use in diagnostic procedures.

Sequencing of SureCell™ WTA 3’ Libraries

Page 17: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

18

Sequencing Conditions for SureCell 3’ Libraries

For Research Use Only. Not for use in diagnostic procedures.

Page 18: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

19

How much sequencing will I need?

5000

50,000

4000

3000

2000

250,000100,000 500,000 1,000,000

6000

25,000

Range depends on cell type and expression levelsand also the biological question you’re asking

# of reads per cell

# of

gen

es d

etec

ted

per c

ell

(APP

RO

XIM

ATE)

● How many genes do I want to detect per cell?

● Am I looking for potentially rare cell types?

● Saturating the number of detected genes requires more reads

For Research Use Only. Not for use in diagnostic procedures.

Page 19: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

20

Sequencing Power for Every Scale

Decreasing price per GB

Incr

easi

ng s

yste

m o

utpu

t & p

rice

HiSeq® 25001000 Gb | 4B

2x125NextSeq®120 Gb | 400M

2x150MiSeq®15 Gb | 25M

2x300

HiSeq 3000750 Gb | 2.5B

2x150

HiSeq 40001500 Gb | 5B

2x150

HiSeq X Ten18000 Gb | 60B

2x150

HiSeq X® Five9000 Gb | 30B

2x150

MiniSeq™7.5 Gb | 25M

2x150

Single Cell RNA-Seq

NovaSeq 6000 S22000 Gb | 6.7B

2x150

For Research Use Only. Not for use in diagnostic procedures.

Page 20: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

21

Sequencing cost per cell2017 USD List

5000

50,000

4000

3000

2000

250,000100,000 500,000 1,000,000

6000

25,000

# of reads per cell

# of

gen

es d

etec

ted

per c

ell

(APP

RO

XIM

ATE)

$6.96

$3.48$1.74

$0.69

$0.35

$0.18

NextSeq 500

For Research Use Only. Not for use in diagnostic procedures.

Page 21: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

22

Sequencing cost per cell2017 USD List

5000

50,000

4000

3000

2000

250,000100,000 500,000 1,000,000

6000

25,000

# of reads per cell

# of

gen

es d

etec

ted

per c

ell

(APP

RO

XIM

ATE)

$4.50

$2.25$1.12

$0.44

$0.23

$0.11

HiSeq 3000

For Research Use Only. Not for use in diagnostic procedures.

Page 22: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

23

5000

50,000

4000

3000

2000

250,000100,000 500,000 1,000,000

6000

25,000

# of reads per cell

# of

gen

es d

etec

ted

per c

ell

(APP

RO

XIM

ATE)

$4.10

$2.05$1.02

$0.41

$0.20

$0.10

NovaSeq S2

For Research Use Only. Not for use in diagnostic procedures.

Sequencing cost per cell2017 USD List

Page 23: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

24

What about data analysis?

For Research Use Only. Not for use in diagnostic procedures.

Page 24: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

25

● Simple analysis setup for samples across multiple sequencing runs- Up to 96 samples per analysis

● Easily choose analysis parameters- Reference genome- ERCC spike-ins- Subsampling for QC

● Rapid alignment, cell and gene counting, and filtering

BaseSpace® Single-Cell RNA App

For Research Use Only. Not for use in diagnostic procedures.

Page 25: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

26

● Per-sample reports available in-browser and as PDF- Alignment quality- Coverage information- Abundant sequences

● Perform global PCA and tSNE clustering

● Cell-cycle heatmap

● All output files available for download, or as input into downstream applications- Includes cell-gene expression table

BaseSpace® Single-Cell RNA App

For Research Use Only. Not for use in diagnostic procedures.

Page 26: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

27

tSNE analysis identifies a sub-population in a heterogeneous cell mixture mouse/human

For Research Use Only. Not for use in diagnostic procedures.

Page 27: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

28

PCA clustering of 1:1 mixture of 1,400 mouse and human cells detects distinct populations

For Research Use Only. Not for use in diagnostic procedures.

Page 28: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

29

Two-species cell mixture (HEK293/NIH3T3) demonstrates low crosstalk and high purity

Cells: 1384Duplets: 5.8%Purity: 99.1%

Number of UMIs Aligned to hg19 Genes

Num

ber o

f UM

Is A

ligne

d to

mm

10 G

enes

For Research Use Only. Not for use in diagnostic procedures.

Page 29: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

30

tSNE axis 1

tSN

E a

xis

2

Platelets(0.8%)

B-Cells (9.0%)

NK cells(11.4%)

Dendritic cells(1.2%)

CD14+ Monocytes(17.6%)

CD16+ Monocytes (5.4%)

Memory T-Cells(12.7%)

Cytotoxic T-Cells (13.4%)

Naïve CD4 &Naïve CD8T-Cells (15.2%)

t-SNE clustering

6,000 cells

4 cartridges

~20m of hands on time for barcoding

Major subclasses of peripheral blood mononuclear cells (PBMCs) identified down to <1%

60,000 reads per cell

Sub-populations identification in PBMCs

For Research Use Only. Not for use in diagnostic procedures.

Page 30: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

31

● Import cell-gene expression tables from BaseSpace

● Discover and characterize populations with gene sets

● Extended heatmappingcapabilities

Further Analysis with 3rd party software

Page 31: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

32

System performance on reference cells

For Research Use Only. Not for use in diagnostic procedures.

Page 32: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

33

Sensitivity & Reproducibility Across Cell Lines

Reads Per Cell (x1,000)

Hum

an G

enes

Det

ecte

d

Mou

se G

enes

Det

ecte

d

Reads Per Cell (x1,000)

Replicate 1 Gene Count

Rep

licat

e 2

Gen

e C

ount R2: 0.975

NumGenes: 10,011

Gene Count Reproducibility

HEK293 Genes vs. Reads Per Cell NIH3T3 Genes vs. Reads Per Cell

Genes Detected Across Different Cell Sizes

Med

ian

Gen

es D

etec

ted

Average Cell Diameter, µm

A20 3T3 HEK BJ

For Research Use Only. Not for use in diagnostic procedures.Illumina internal data on file

Page 33: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

34

Correlation between ddPCR and ddSEQ

R² = 0.810

-8

-6

-4

-2

0

2

4

6

8

0 5 10 15 20

Nor

mal

ized

ddP

CR

log2

3D

Ex

pres

sion

ddSEQ log2 3D Expression (FPKM)

R² = 0.789

-10-8-6-4-20246

8

0 5 10 15 20N

orm

aliz

ed d

dPC

R lo

g2 2

D

Expr

essi

on

ddSEQ log2 2D Expression (FPKM)

Good correlation between bulk and aggregate single cell data

Data courtesy of Drs. David Schaffer & Maroof AdilUniversity of California, Berkeley

Department of Chemical & Biomolecular Engineering

For Research Use Only. Not for use in diagnostic procedures.

Page 34: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

35

ddSEQ SCI & SureCell Kit Future Scalability

More sensitivity through target enrichment

More cells, same robust assay

1 be

ad

0 be

ad

> 1

bead

1 be

ad

0 be

ad

> 1

bead

Random (Poisson statistics)

Dro

plet

Occ

upan

cy

80%

70%

60%

50%

40%

30%

20%

10%

0%

More assays for single cell characterization

For Research Use Only. Not for use in diagnostic procedures.

Page 35: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

36

Illumina | Bio-Rad Single Cell Sequencing Solution

1. Isolation and barcoding of several thousand single cells in minutes2. Affordable platform3. Scalable to profile increasing number of cells in a cost-effective manner4. Proven Illumina library prep with streamlined workflow5. Single-Cell RNA-Seq BaseSpace® App available

For Research Use Only. Not for use in diagnostic procedures.

Page 36: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

37

Sensitive

Accurate

Scalable

Simple

Reproducible

Integrated

5-7K genes per cell

No pre-amp, correlates with orthogonal method (ddPCR)

Kit formats to support 102-104 cells per day

Nextera. Easy stopping points, sequence the second day

High correlation experiment to experiment

Built-in setup and analysis. End-to end solution

A solution to meet your needs

Page 37: Illumina®|Bio-Rad® Single Cell Sequencing Solution...Single Cell Isolation Principle Single-Cell Suspension Cell Isolation Reagents (including barcodes) Isolate thousands of cells

© 2016 Illumina, Inc. All rights reserved.Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DesignStudio, Epicentre, ForenSeq, Genetic Energy, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan, iSelect, MiniSeq, MiSeq, MiSeqDx, MiSeq FGx, NeoPrep, NextBio, Nextera, NextSeq, Powered by Illumina, SureMDA, TruGenome, TruSeq, TruSight, Understand Your Genome, UYG, VeraCode, verifi, VeriSeq, the pumpkin orange color, and the streaming bases design are trademarks of Illumina, Inc. and/or its affiliate(s) in the US and/or other countries. All other names, logos, and other trademarks are the property of their respective owners.

Thank you