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Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

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Page 1: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 1

Overview on Agilent Lab on a Chip

Applications

2100 Bioanalyzer SolutionsMarch 2007

Page 2: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 2

The Lab-on-a-Chip Approach

Active Control of Fluids without Moving Parts

Sample volumes 1 -4 µl

10 -12 samples depending on Assay

Separation, staining, detection of samples

Results in 5-30 minutes available

No extra waste removal needed

Disposable Chip, no crosscontamination

Page 3: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 3

Lab-on-a-Chip or Gel - A Faster Answer !

Page 4: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 4

Agilent 2100 Kits and consumables

Various Kits and consumables are availableto support the predefined methods o the2100 BioanalyzerAgilent RNA 6000 Nano Kit 5067-1511Agilent RNA 6000 Nano Reagents 5067-1512 Agilent RNA Nano Ladder 5067-1529Agilent RNA 6000 Pico Kit 5067-1513 Agilent RNA 6000 Pico Reagents 5067-1514Agilent RNA Pico Ladder 5067-1535Agilent DNA 1000 Kit 5067-1504 Agilent DNA 1000 Reagents 5067-1505 Agilent DNA 7500 Kit 5067-1506Agilent DNA 7500 Reagents 5067-1507Agilent DNA 12000 Kit 5067-1508Agilent DNA 12000 Reagents 5067-1509Agilent Protein 230 Kit 5067-1517Agilent Protein 230 Reagents 5067-1518Agilent Protein 80 Kit 5067-1515Agilent Protein 80 Reagents 5067-1516Agilent Cell Kit 5067-1519Agilent Cell Checkout Kit 5067-1520

Page 5: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 5

RNA Applications

RNA QA/QC for

Microarrays

Gene Expression

Genomic DNA

ContaminationRNA QA/QC

for qPCR

RNA QA/QC for mPCR

smallRNA QA/QC

Page 6: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 6

Analytical Specification total RNA mRNA

Qualitative Range 5-500ng/ul 25-250ng/ulQuantitative Range 25-500ng/ul 25-250ng/ul

Reproducibility of Quantitation 10% CV 10% CVMaximum Sample

Buffer Strength 10 mM Tris-EDTA 10 mM Tris-EDTA

Physical Specification

Analysis Time 30 minutes 30 minutesNumber of Samples 12 samples/chip 12 samples/chipSample Volume 1ul 1ulAssay Kit Stability 4 months at 4 C 4 months at 4 C

Specifications RNA assays (Series2 assays)

Analytical Specification total RNA mRNA

Qualitative Range 50-5000 pg/µl 250-5000 pg/µlMaximum Sample

Buffer Strength 50 mM Tris or NaCl 50 mM Tris or NaCl

Physical Specification

Analysis Time 30 minutes 30 minutesNumber of Samples 11 samples/chip 11 samples/chipSample Volume 1 µl 1 µlAssay Kit Stability 4 months at 4 C 4 months at 4 C

RNA 6000 Nano LabChip kit RNA 6000 Pico LabChip kit

Page 7: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 7

total RNA

determine integrity and quality of total RNA

determination of RNA concentration

identify ribosomal peaks

calculate the ratio of ribosomal peaks (18S/28S or 16S/23S)

RNA integrity number (RIN)

mRNA

determine integrity and quality of mRNA samples

Determination of mRNA concentration

calculate % ribosomal RNA in mRNA samples

Features of the RNA 6000 Assays

Page 8: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 8

RNA 6000 Nano LabChip kit Analysis of Total RNA Integrity

High quality total RNA

Partially degraded total RNA

18S

28S

Flu

ores

cenc

e

Time (seconds)

0

1

2

3

4

5

6

7

8

9

10

11

19 24 29 34 39 44 49 54 59 64 69

marker18

S

28S

Flu

ores

cenc

e

Time (seconds)

0

1

2

3

4

5

6

7

8

9

10

11

19 24 29 34 39 44 49 54 59 64 69

marker

28S18S Typical first QC step after RNA sample prep prior to microarrays or real-time PCR

2100 bioanalyzer: electropherogram

2100 bioanalyzer: single lane gel-like image

Page 9: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 10

RNA QC in Routine Gene Expression Workflow

Start again with sample isolation

Cells / Culture

RNA isolation

Total RNA

RIN

RNA QC via Agilent 2100 bioanalyzer

RIN above threshold

Continue with downstream Experiment (Microarray, real-time PCR, etc.)

Page 10: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 11

108 samples 3 dilutionsCV RIN: 3 %CV ribosomal ratio: 22 %

108 samples 3 dilutionsCV RIN: 3 %CV ribosomal ratio: 22 %

RIN Application – Directly Compare Samplessame sample in different dilutions

18S

28S

Flu

ores

cenc

e

0.0

2.5

5.0

7.5

10.0

12.5

18S

28S

Flu

ores

cenc

e

Time (seconds)

0

10

20

30

40

50

60

70

80

19 24 29 34 39 44 49 54 59 64 69

18S

28S

Flu

ores

cenc

e

0

5

10

15

20

25 ng/µl: RIN 8

100 ng/µl: RIN 8

500 ng/µl: RIN 8

When testing an identical RNA sample in various dilutions, identical RINs are obtained – within narrow limits

Page 11: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

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RIN Application – Assessment of RNA Integrity

Intact RNA: RIN 10

Partially degraded RNA: RIN 5

Strongly Degraded RNA: RIN 3

18S

28S

Flu

ores

cenc

e

0

1

2

3

4

5

6

7

8

9

18S

28S

Flu

ores

cenc

e

0

5

10

15

20

25

30

35

40

45

Flu

ores

cenc

e

Time (seconds)

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

19 24 29 34 39 44 49 54 59 64 69

Page 12: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 13

18S

28S

Flu

ores

cenc

eTime (seconds)

0.0

2.5

5.0

7.5

10.0

12.5

16 21 26 31 36 41 46 51 56 61 66 71 76 81

18S

28S

Flu

ores

cenc

e

Time (seconds)

-0.5

0.0

0.5

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

5.0

5.5

21 26 31 36 41 46 51 56 61 66 71 76 81

rRNA contamination: 19.5 %

rRNA contamination: 1.7 %

Mou

se k

idne

y I

mR

NA

Mou

se k

idne

y II

mR

NA

Rat

bra

in m

RN

A

Bov

ine

kidn

ey m

RN

A

Mou

se t

esti

s m

RN

A

Mou

se li

ver

mR

NA

RN

A 6

000

ladd

er

Ribosomal RNA contamination in mRNA samples

Page 13: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 14

Laser Microdissection and Pressure Catapulting (LMPC)

RNA extraction

A

B

C

RNA sample QC using the Agilent 2100 bioanalyzer and the RNA 6000 Pico LabChip kit

Laser Microdissection – PALM MicroBeam System

Data kindly provided by P.A.L.M. Microlaser Technologies

Laser microdissection

Laser pressure catapulting: Section after catapulting of selected area

Catapulted area in the collection device

18S

28S

24 29 34 39 44 49 54 59 64 69

200 pg total RNA

200 pg total RNA

Page 14: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 15

cRNA fragmentation

Cy3/ Cy5 Labeling

Total RNA QC

mRNA QC

Array experiment

cRNA Hybridization - Workflow

Data evaluation

Page 15: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 16

Series II RNA AssaysA new RNA Ladder is now included in the kit.

Improved quantitation accuracy with salt containing samples. No late migration of 28S peaks

Pico: higher sensitivity, better reproducibility and accuracy in quantitation

- Higher reagent volumes at no charge

new old

Page 16: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 17

RNA Con’tIncreased sensitivity, Pico Assay

50 pg/µL total RNA in water (Series II RNA 6000 Pico assay)

Page 17: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 18

Analysis of Small RNA (using RNA 6000 Assay)

Small RNA fraction: < 200 nts e.g. miRNA, siRNA, snRNA, tRNA, 5S RNA

Bioanalyzer allows discrimination of different profiles

Page 18: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 19

Small RNA Assay specifications

Analytical Range                  6 -150 nt (to avoid overlap)

Sensitivity 50 pg/µl  

(diluted Ladder - 40 nt fragment; S/N > 3:1)

Quantitative range 50 pg/µl – 2000 pg/µl

(purified miRNA in water after extraction ~<200nt)

Quantitation Reproducibility 25 % CV

(defined on Ladder)

Max amount total RNA 100 ng/µl total RNA

Carryover         Below detection limit

Page 19: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 20

miR

NA

tRN

A

Small rRNAsL

ower

Mar

ker

[nt]

New Small RNA Assay

Fragments larger than 200nt (i.e. 18S/28S) are not injected and do not interfere with the assay

Lo

we

r M

ark

er

50

bp

tRNA

18s rRNA 28s rRNA

RNA 6000 Assay

Small RNA Assay

Two complimentary assays, one to evaluate total RNA integrity and the second to characterize the small RNA fraction

Page 20: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 21

Sm

all

RN

A R

eg

ion

New Small RNA Assay versus existing RNA Assay

miR

NA

Re

gio

n

Lo

wer

Mar

ker

Small RNA Region

tRN

A

18s

28s

RIN: 8.1

Lo

wer

Mar

ker

RNA 6000Nano kit

Small RNA Kit

RNA 6000Nano

Size range: 25-6000nt

Results: Integrity, Total RNA amount, gDNA contamination

NEW! Small RNASize range: 6-150nt

Results: miRNA amount, Ratio and amount of other Small RNA

5s

5.8s

Page 21: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 22

Protein Applications

AntibodyQA/QC

Protein Expression

Protein Purification

Food Analysis

ProteinQA/QC

Compliant Protein & AntibodyQA/QC

Page 22: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 23

Protein LabChip Kits – Specifications (Series II)

• Automated analysis of 10 protein samples in less than 30 minutes

• Two assays for complementary size ranges

– Protein 80: 5 to 80 kDa – Protein 230: 14 to 230 kDa

• Sizing resolution of 10% across the size range

• Large linear dynamic range (e.g. from 15 - 2000 ng/l CA-II in PBS)

• Sensitivity equivalent to non-colloidal Coomassie (R-250) stain

• Relative and absolute quantitation

• Compatible to a variety of sample buffer components

Page 23: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 24

Protein Series II Assay - Specs

Parameter Protein 230 Protein 80

Analysis time [min] 25 30No of samples 10 10Sample vol [µl] 4 4

Sizing range [kDa] 14 - 230 5 - 80Typical sizing resolution 10% 10%Typical sizing accuracy 10% CV 10% CVSizing reproducibility 3% CV 3% CVSensitivity CAII 6ng/µl 6ng/µlSensitivity BSA 15ng/µl 15ng/µlQuantitative range [ng/µl] CAII 15 - 2000 60 - 2000Qualitative range [ng/µl] CAII 6 - 5000 6 - 4000Quantitation reproducibility 20% CV 20% CV

Page 24: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 25

Staining, Destaining and DetectionStaining, Destaining and Detection

protein

micelles

destain

SDS + dye

detection

low background good signal to noise ratio SDS conc. below CMC

If no dilution was done the micelles would result in high background and low sensitivity

detection

X

Page 25: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 26

Staining, Destaining and DetectionStaining, Destaining and Detection

protein

micelles

SDS + dye

destain

detection

low background good signal to noise ratio SDS conc. below CMC

Page 26: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 27

Protein LabChip Applications

Cell lysates• identification of over-expressed proteins• comparison of different expression patterns

Column fractions• monitoring of protein isolation and purification process• check fractions for impurities

Purified proteins• monitoring of impurities in protein preps• integrity check for monoclonal or polyclonal antibodies

(antibody QC)

Page 27: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 28

Clone Selection based on Protein Expression

1* 2 3 4 5 6 7 8*

Flu

ores

cenc

e

Time (seconds)

0

10

20

30

40

50

60

20 25 30 35 40 45 50 55

colony 1 colony 2

53.0

21.5

29.032.5

14.4

6.0

kDa

protein of interest

Example measured withProtein 50 kit

Page 28: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 29

Monitoring of Protein Purification Process

2100 bioanalyzer: gel-like image Courtesy of P. Sebastian and S.R. SchmidtGPC-Biotech AG, Martinsried, Germany

cell lysate

wash(fraction 69)

elution (fraction 77)

flow through(fraction 66)

wash (fraction 78)

Time (seconds) 15 20 25 30 35 40 45

GFP Fusion Protein Analysis

2100 bioanalyzer: electropherogram

Example measured withProtein 200 plus kit

Page 29: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 30

Protein P230 Series II Assay

Assay reworked for optimized stability

– Sizing range from 14-230 kDa

– UM at 240 kDa

– New lower marker and optimized LM detection (less overlap with system peak)

– New ladder

– Baseline stability and better sensitivity

High purity UM and ladder improves usability in QC (optimized for low level impurity quantification -> compliance).

Page 30: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 31

Quality Control of Antibodies

90 kDa 160 kDa

intact antibody

16% half antibody

Determine the half antibody content in IgG preparations

Antibody analysis under reducing and non-reducing conditions

Ab reduced

Ab non-reduced

light chain

heavy chain

intact antibody

light + heavy chain

Ab reduce

d

Ab non-reduce

d

Absolute Quantitation of IgG samples

Page 31: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 32

Protein 80 Series II assay

• sizing range 5-80 kDa (specific fit to antibody QC)

• new ladder & new UM

• improvements in sensitivity (sizing/quantitation)

• improvements in sensitivity specifications as P230

PBS blank runladder run

Page 32: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 33

2100 Bioanalyzer Compliance

2100 expert software- One version for all assays- Declaration of system validation

2100 expert security pack- 21 CFR part 11compliance- Electronic records- Electronic signatures- Audit trails

2100 bioanalyzer - IQ and OQ/PV services- Declaration of conformity

Chips and reagents- Declaration of conformity

Page 33: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 34

DNA Applications

mtDNA Screening

qPCR validation, impurity check

mPCR validation, impurity check

Restriction Digest

Analysis

Gene Expression

Oncology

Food Analysis

Clinical Research

ForensicTesting

Page 34: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 35

Application Areas for the DNA Assays

PCR product purity

Multiplex PCR Applications

Gene expression analysis via RT-PCR (target validation)

GMO testing

Pathogen detection (homeland defense, hospitals, environmental)

Genotyping applications

• Duplications/ deletions

• Allele frequency

• Bacterial sub-typing

• Forensics

Cancer diagnostics

Page 35: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 36

marker

marker

25 bp

473, 500 bp

100, 105 bp

300, 315 bp

900, 1000 bp

2100 bioanalyzer dataGel-like image

25 bp

473, 500 bp

100, 105 bp

300, 315 bp

900, 1000 bp

2 % agarose gel stainedwith Ethidiumbromide

Data Format - Gel-Like Image c/w Agarose Gel

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Group/Presentation TitleAgilent Restricted Month ##, 200XPage 37

1 2 3 4 5

20001200

200

800

400

100

1 2 3 4 5

20001200

200

800400

100

Agilent 2100 bioanalyzer

Agarose gel

300 bp

3000 bp

Determination of PCR Product Impurity

Page 37: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 38

Quantitative data from Agilent 2100 bioanalyzer

Sample c (DNA) main peak

300 bp PCR 41.4 ng/ul 40.7 ng/ul 300 bp PCR 1:4 9.6 ng/ul 9.6 ng/ul

Quantitative data from Agilent 2100 bioanalyzer

Sample c (DNA) main peak

300 bp PCR 41.4 ng/ul 40.7 ng/ul 300 bp PCR 1:4 9.6 ng/ul 9.6 ng/ul

1* 2 3 4 5 6 7*

Fluo

resc

ence

Time (seconds)

0

100

200

300

400

500

25 30 35 40 45 50 55 60 65 70 75 80 85 90

3000 bp PCR 3000 bp PCR 1:4 dil.

Impurity level : > 50%

3000 bp

Determination of PCR Product Impurity

1* 2 3 4*

Fluo

resc

ence

Time (seconds)

0

100

200

300

400

500

25 30 35 40 45 50 55 60 65 70 75 80 85 90

300 bp PCR 300 bp PCR 1:4 dil.

Impurity level : < 2%

300 bp

Quantitative data from Agilent 2100 bioanalyzer

Sample c (DNA) main peak

3000 bp PCR 61.9 ng/ul 40.7 ng/ul3000 bp PCR 1:4 14.8 ng/ul 9.8 ng/ul

Quantitative data from Agilent 2100 bioanalyzer

Sample c (DNA) main peak

3000 bp PCR 61.9 ng/ul 40.7 ng/ul3000 bp PCR 1:4 14.8 ng/ul 9.8 ng/ul

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Group/Presentation TitleAgilent Restricted Month ##, 200XPage 39

GMO Detection: Determination of GM Soya Percentage

Data kindly provided by CCFRA

Soya lectin gene target

EPSPS gene target: specific for Roundup Ready GM soya (Monsanto)

Page 39: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 40

Effect of Multiplex PCR buffer on a 19-plex PCR

Data kindly provided by QIAGEN GmbH, Germany

Page 40: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 41

Tumor Diagnostics

Data kindly provided by Adnagen

1. Spiking experiment with given amount of cancer cells

2. Enrichment with AdneGen Cancer Select kit (antibody based immunomagnetic enrichment.)

3. Multiplex Amplification with AdnaGen CancerDetect kit

4. Detection with Agilent 2100 Bioanalyzer and DNA 500 LabChip kit

Page 41: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 42

Detection of Single Base Mutations (1)in Exons 7 and 8 of the Human p53 Gene by RFLP Mapping using the DNA 7500 kit

Amplify exons 7 and 8 (resulting products: 618 bp fragment and 200 bp fragment)

Digest with Hpa II

Analyze using Agilent 2100 bioanalyzer and 4-20 % acrylamide gel

exon 7 exon 8

83 bp, 91 bp,168 bp, 276 bp

91 bp, 109 bpIn each example one of the restriction sites can be deleted by a point mutation

Page 42: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 43

Detection of Single Base Mutations (2)

wt 106

200 bp109 bp

91 bp

91 bp91+83 bp

168 bp

wt 59

276 bp276 bp

251 bp

1*

2 3 4 5*

0

5

10

15

20

25

30

Flu

ore

sce

nce

Time (seconds)

30 35 40 45 50 55 60 65 70 75

p53Exon 7 wt/HpaII p53Exon 7 clone 59/HpaII

Lower Marker

Upper Marker267/268 bp

251 bp

166 bp

84/85 bp

1*

2 3 4*

0

5

10

15

20

25

Flu

ore

sce

nce

25 30 35 40 45 50 55 60 65

p53Exon 8 wt/HpaII p53Exon 8 clone 106/HpaII

Lower Marker

Upper Marker

Time (seconds)

208 bp111 bp

90 bp

Page 43: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 44

Label free Analysis of Microsatellite InstabilitiesClinical Diagnostics and Molecular Diagnostics of Cancer

Microsatellite instabilities present in 10-15% of colon and gastric carcinomas

Study: 40 cases of colon carcinoma

5 microsatellite loci investigated

Results compared with traditional PAGE:

95% concordance rate

Page 44: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 45

Cell Applications

Protein Expression Monitoring

Intracellular

Transfection Efficiency Monitoring

Apoptosis Detection

Gene Silencing

Protein Expression Monitoring

Cell Surface Antibody Staining

Page 45: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 46

Cell Assay

Apoptosis

Transfection Efficiency Monitoring

• Detection of GFP-transfected cells• Antibody staining: Detection of transfected cells expressing the encoded

protein

Protein Expression Monitoring

• Extracellular and Intracellular Antibody staining for detection of protein expressed on the cell surface, in the cytoplasm, or in the nucleus

Gene silencing

Page 46: Group/Presentation Title Agilent Restricted Month ##, 200X Page 1 Overview on Agilent Lab on a Chip Applications 2100 Bioanalyzer Solutions March 2007

Group/Presentation TitleAgilent Restricted Month ##, 200XPage 47

Principle of Pressure-Driven FlowFor cell assays (analysis of cell fluorescence parameters)On-chip simple flow cytometric studies

Pressure driven flow is used to move cells in a controlled manner through the micro-channels

Cells are hydrodynamically focused to a portion of the channel by a side stream of buffer

Cells pass the fluo-rescence detector in single file and each event is monitored in a histogram or dot plot

The micro-channels of the glass chip are filled with cell buffer

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Group/Presentation TitleAgilent Restricted Month ##, 200XPage 48

The Bioanalyzer Lab-on-a-Chip ApproachSeparation on disposable, µ-fabricated glass chips

• made of two glass layers:• one with micro-channels (x10µm, etched),• one with through-holes

• glued into a plastic caddy which accommodates wells for gel, sample, standard (ladder), buffer and other reagents • for handling nl-amounts of liquids• one separation channel for ladder and sample• microfluidic sample movement with fluorescence detection

Setup• micro-channels are filled with gel or buffer• sample, ladder and reagents are filled into the respective wells•chip preparation in less than 5 minutes

Benefits• convenient handling• minimized risk of cross-contamination• versatile design for multiple experiments on one platform

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Flow Cytometry on a Chip - Hydrodynamic Focusing

All six cell samples are hydrodynamicly focused to one side of the micro channel

At each of the six pinch points the cell stream is joined by a buffer stream from one of the two buffer wells

The two liquids do not mix immediately

The cells then move towards the detector in single file

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Flow Cytometry on a Chip - Two Color Detection- Three Types of Events

Blue/red cellsRed cells Blue cells

Dot plot view for easydata evaluation

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Some Target applications

Apoptosis:

Annexin V Detection of phosphatidylserine on the cell surface

Caspase-3 Detection of activated caspase-3 in the cytoplasm

Transfection Efficiency Monitoring:

GFP: Detection of GFP-transfected cells

Antibody staining: Detection of transfected cells expressing the encoded protein

Protein Expression Monitoring:

Extracellular and Intracellular Antibody staining for detection of protein expressed on the cell surface, in the cytoplasm, or in the nucleus

Gene silencing:

Optimization of siRNA transfection procedureVerify silencing by cellular protein expression measurementCorrelation of siRNA uptake and gene knockdown

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Typical workflow:

Cell assays: sample preparation

adherent

suspension(trypsinize) & harvest by centrifugation, wash

wash twice

Resuspend cells in cell buffer (LabChip Kit)

Load on chip

Add staining reagentand incubate

Data analysis to result

Customer Agilent

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2100 Bioanalyzer

Red detection channel:

• 620-645 nm excitation with Laser (Maximum 630 nm)

• 674-696 nm detection range (Maximum 680 nm)

Blue detection channel:

• 458-482 nm excitation with LED (Maximum 470 nm)

• 510-540 nm detection range (Maximum 525 nm)

Flow Cytometry on a Chip - Optics & Detection

Standard Flow Cytometers have 3-4 fluorescence detection channels:FL1: excitation 488 nm, detection 530 nmFL2: excitation 488 nm, detection 585 nmFL3: excitation 488 nm, detection 661 nmFL4: excitation 635 nm, detection 670 nm

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Cell Assays - Applications: ApoptosisAnnexin Binding

Phosphatidyl-serine from inner leaflet flips to outer membrane Phosphatidyl-serine from inner leaflet flips to outer membrane during apoptosis and can be labeled by Annexin Vduring apoptosis and can be labeled by Annexin V

Healthy cellHealthy cell

““Live” apoptotic cellLive” apoptotic cell

Dead cellDead cell

Live dye: Calceinbiotin-Annexin+ Cy5-streptavidin

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Annexin V Assay (24h Induction)

0%

20%

40%

60%

80%

0 10 20 30

Sample Number

% A

po

pto

tic

2100-1

2100-2

2100-3Flow cytometer

5 chips, each loaded with control in well 1 and 24h sample in wells 2-6

Three Bioanalyzer instruments vs a flow cytometer reference instrument

Chip 1 Chip 2 Chip 3 Chip 4 Chip 5

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Applications: Protein Expression AnalysisGFP Transfection Efficiency Control

Disclaimer. Neither Agilent nor Caliper makes any representation that use of EGFP andpractice of the methods described in this publication is licensed orotherwise authorized under any third party patents, including patents ownedor exclusively licensed by Aurora Biosciences or Amersham Biosciences.

CHO-K1 cells were transfected with EGFP DNA and Lipofectamine.

GFP transfected cells

Mock transfected cells

0.1 %

56.6 %

Control

EGFP transfected

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GFP Transfection Efficiency

0%

10%

20%

30%

40%

50%

60%

70%

1 2 3 4 5

Chip Number

Tra

ns

fec

tio

n E

ffic

ien

cy

Flow cyt.

2100-1

2100-2

2100-3

2100-1 2100-2 2100-3 All Flow cyt.ctrl mean 0.46 0.31 0.47 0.40 0.16

SD 0.08 0.29 0.43 0.29 0.12

GFP mean 60.19 59.15 59.26 59.53 60.90SD 2.13 2.48 2.10 2.26 1.22

%CV 3.54 4.19 3.54 3.80 2.01

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Flow Cytometry Assays Applications - Cell surface Antibody staining

Cell expressingprotein of interest

Target protein

Live dye: CalceinCy5 or APC-labeled Antibody

Cell not expressingprotein of interest

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Extracellular Antibody Staining

Averaged data per instrument

0.00

10.00

20.00

30.00

40.00

50.00

60.00

70.00

80.00

1 2 3 4 5 6

sample #

% g

ated

% gated 2100-1

% gated 2100-2

% gated 2100-3

%gated 2100-4

Flow cytometer

Jurkat cells were stained with calcein alone or with calcein and APC-labeled anti-CD3 antibody. Mixtures of both populations were prepared at various ratios.Samples were analyzed with four 2100 instruments on 5 chips and compared to a flow cytometer reference instrument

Mean % CD3+ cells2100-1 2100-2 2100-3 2100-4 Flow cyt.60.9 67.8 66.6 65.0 60.934.4 36.7 36.7 34.3 29.817.3 17.6 18.7 17.2 13.88.9 9.4 9.9 8.3 6.55.1 4.4 5.3 4.9 3.20.8 0.6 0.3 0.3 0.0

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GFP On-Chip Staining - Histogram Quality

2100 bioanalyzer

Flow Cytometer