1005200_Sequencing_LTW_PairedEnd_GA2_v3 Sequencing LTF Paired End GA2 1005200 Rev B

Sequencing_LTF_Paire.. Sequencing_LTF_PairedEnd_GA2_1005200_RevB

User Manual: Sequencing LTF PairedEnd GA2 1005200 RevB

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Page Count: 9

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 1 of 9

Flow cell ____________________

Run folder ____________________

1 Samples Loaded

Lane Sample ID Concentration (pM)

1 Sam

ple

1 Con

c. 1

2 Sam

ple

2 Con

c. 2

3 Sam

ple

3 Con

c. 3

4 Sam

ple

4 Con

c. 4

5 Sam

ple

5 Con

c. 5

6 Sam

ple

6 Con

c. 6

7 Sam

ple

7 Con

c. 7

8 Sam

ple

8 Con

c. 8

2 Cluster Generation

Step Date

Amplification

Linearization, Blocking, and Primer

Hybridization for Read 1

Paired-End Cluster Generation Kit v2 Lot Numbers

Reagent Lot Number

AMX1

AMX2

AT1

AT2

BMX

EMX

HP1

HP2

HP3 (Read 1)

HP2 (Read 2)

HT1

HT2

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 2 of 9

Reagent Lot Number

LMX1

LMX2

RMX

Reagent Volumes After Amplification

Position Reagent Volume

1 AMX1

3 HT2

9 AT1

12 HT1

Reagent Volumes After Linearization, Blocking, and Primer Hybridization

Position Reagent Volume

3 HT2

4 BMX

7 HP1

12 HT1

14 LMX1

17 HP3

3 Preparing Sequencing Reagents for Read 1

SBS Sequencing Kit v3 Lot Numbers

Reagent Lot Number

IMX

FFN

SDP

CLM

SMX

PR1

PR2

PR3

PW1

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 3 of 9

4 Pre-Run Wash

Expected Volume Delivered Volume

12 ml

5 Loading and Priming Reagents

Weights of Material Delivered

Position Reagent Weight Before Run Weight After Run Delivered Weight

1 IMX

2 PW1

3 SMX

4 PR1

5 PR2

6 CLM

7 PR3

Priming Reagents

Expected Volume Delivered Volume % Difference

6.4 ml

6 Checking for Leaks and Reagent Delivery

Port Position 5

Expected Volume: 800 μl

Measured Volume 1: ____________________

Measured Volume 2: ____________________

Measured Volume 3: ____________________

% Difference Between

Expected Volume and

Measured Volume 3: ____________________

0.00

0.00

0.00

0.00

0.00

0.00

0.00

-100.00

-100

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 4 of 9

7 Setting Best Focus for Channel A, Read 1

Z Position FQ Value

1 A300 1 C300

2 A200 2 C200

3 A100 3 C100

4 A0 4 C0

5 A-100 5 C-100

6 A-200 6 C-200

7 A-300 7 C-300

Position of Z for Lane 4: _____________________

8 Adjusting Focus

FQ Calculation

Z Position A C G T Total

A70

0 C70

0 G70

0 T70

0 TOT7

00

A60

0 C60

0 G60

0 T60

0 TOT6

00

A50

0 C50

0 G50

0 T50

0 TOT5

00

A40

0 C40

0 G40

0 T40

0 TOT4

00

300 A30

0 C30

0 G30

0 T30

0 TOT3

00

200 A20

0 C20

0 G20

0 T20

0 TOT2

00

100 A10

0 C10

0 G10

0 T10

0 TOT1

00

0 A0 C0 G0 T0 TOT0

-100 A-

100 C-

100 G-

100 T-

100 TOT-

100

-200 A-

200 C-

200 G-

200 T-

200 TOT-

200

-300 A-

300 C-

300 G-

300 T-

300 TOT-

300

A-

400 C-

400 G-

400 T-

400 TOT-

400

A-

500 C-

500 G-

500 T-

500 TOT-

500

A-

600 C-

600 G-

600 T-

600 TOT-

600

A-

700 C-

700 G-

700 T-

700 TOT-

700

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 5 of 9

9 Performing Post-Run Procedures for Read 1

Run Fluid Delivery Data

Lane Weight of Empty Tube Weight of Tube After Run Weight of Fluid Delivered

During Run

1

2

3

4

5

6

7

8

10 Read 1 Data Transfer

Step Description Date

1a Images Scan

before Scan

after

1b Focus images (if stored) IM

after

1c Log files IB

before IB

after

1d Configuration files

HSB

before HSB

after

1e Calibration files CM

before CM

after

3 Delete Run Folder CB

before CB

after

11 Loading and Priming Reagents for Read 2 Preparation

Weights of Material Delivered

Position Reagent Weight Before Run (g) Weight After Run (g) Delivered Weight (g)

10 RMX IM before IM

after IM

deliv.

11 LMX2 IB before IB

after IB

deliv.

12 BMX HSB

before HSB

after HSB

deliv.

13 AMX2 CM

before CM

after CM

deliv.

15 AT2 Scan

before Scan

after Scan

deliv.

16 HP2

CM

before IM

after IM

deliv.

0.00

0.00

0.00

0.00

0.00

0.00

0.00

0.00

0

0

0

0

0

0

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 6 of 9

Position Reagent Weight Before Run (g) Weight After Run (g) Delivered Weight (g)

19 HP3 CM

before CM

after CM

deliv.

21 HT2 Water

before Water

after Water

deliv.

Reagent Volumes After Priming and Read 2 Preparation

Position Reagent Volume After Priming Volume After Read 2 Preparation

10 RMX

11 LMX2

12 BMX

13 AMX2

15 AT2

16 HP2

19 HP3

21 HT2

12 Preparing Sequencing Reagents for Read 2

SBS Sequencing Kit v3 Lot Numbers

Reagents Lot Number

IMX

FFN

SDP

CLM

SMX

PR1

PR2

PR3

PW1

1

8

2

3

-1

5

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 7 of 9

13 Loading Sequencing Reagents for Read 2

Weights of Material Delivered

Position Solution Weight before Run Weight after Run Delivered Weight

1 IMX

2 PW1

3 SMX

4 PR1

5 PR2

6 CLM

7 PR3

14 Checking for Leaks and Reagent Delivery

Port Position 5

Expected Volume: 800 μl

Measured Volume 1: ____________________

Measured Volume 2: ____________________

Measured Volume 3: ____________________

% Difference Between

Expected Volume and

Measured Volume 3: ____________________

15 Setting Best Focus for Channel A, Read 2

Z Position FQ value

1 A300 1 C300

2 A200 2 C200

3 A100 3 C100

4 A0 4 C0

5 A-100 5 C-100

6 A-200 6 C-200

7 A-300 7 C-300

Position of Z for Lane 4: _____________________

0.00

0.00

0.00

0.00

0.00

0.00

0.00

-100

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 8 of 9

16 Adjusting Focus for Read 2

FQ Calculation

Z Position A C G T Total

A70

0 C70

0 G70

0 T70

0 TOT7

00

A60

0 C60

0 G60

0 T60

0 TOT6

00

A50

0 C50

0 G50

0 T50

0 TOT5

00

A40

0 C40

0 G40

0 T40

0 TOT4

00

300 A30

0 C30

0 G30

0 T30

0 TOT3

00

200 A20

0 C20

0 G20

0 T20

0 TOT2

00

100 A10

0 C10

0 G10

0 T10

0 TOT1

00

0 A0 C0 G0 T0 TOT0

-100 A-

100 C-

100 G-

100 T-

100 TOT-

100

-200 A-

200 C-

200 G-

200 T-

200 TOT-

200

-300 A-

300 C-

300 G-

300 T-

300 TOT-

300

A-

400 C-

400 G-

400 T-

400 TOT-

400

A-

500 C-

500 G-

500 T-

500 TOT-

500

A-

600 C-

600 G-

600 T-

600 TOT-

600

A-

700 C-

700 G-

700 T-

700 TOT-

700

17 Performing Post-Run Procedures for Read 2

Run Fluid Delivery Data

Lane Weight of Empty Tube Weight of Tube after Run Weight of Fluid Delivered

during Run

1

2

3

4

5

6

7

8

0.00

0.00

0.00

0.00

0.00

0.00

0.00

0.00

Paired-End Sequencing on the Genome Analyzer II

Lab Tracking Form

Part # 1005200 Rev. B Page 9 of 9

Post-Run Wash

Weight of Tube after Wash: ____________________

Weight of Empty Tube: ____________________

Weight of Fluid Delivered: ____________________

18 Sign-off

Date: ____________________

Name: ____________________

Signature: ____________________

0