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Create TruSeq Custom Amplicon or TruSeq Amplicon Cancer
Panel Sample Plates and Sample Sheets with IEM
FOR RESEARCH USE ONLY
This quick reference card describes how to use the Illumina®
Experiment Manager (IEM) to create a TruSeq® Custom
Amplicon or TruSeq Amplicon - Cancer Panel sample plate,
as well as create and edit sample sheets compatible with your
Illumina sequencer and analysis software.
d
7
[Optional] Click the Plate Graphic tab to view the sample
ID and index adapter in each well.
a If you want to copy an image of your sample plate for
use in a presentation or paper, click Copy to
Clipboard on the Plate Graphics tab.
You can paste the image into any graphics-enabled
program, such as Paint, Microsoft PowerPoint,
Microsoft Word, and Adobe Photoshop.
b If you want to print an image of your sample plate,
click Print... on the Plate Graphics tab.
8
Click Finish and save the sample plate file.
For more detailed general information on how to use the
IEM application and definitions of the sample sheet
applications, see the Illumina Experiment Manager User Guide
(part # 15031335).
NOTE
Make sure that you are familiar with the latest version of the
Illumina Experiment Manager User Guide (part # 15031335).
New or less experienced users are advised to read the guide
before using this quick reference card.
Create a Sample Plate
NOTE
A sample plate is not required to generate a sample sheet,
but can be useful for organizing samples.
1
Open the IEM software.
2
On the IEM main screen, click Create Sample Plate.
3
On the Sample Prep Kit Selection screen, select TruSeq
Amplicon for TruSeq Custom Amplicon or TruSeq
Amplicon - Cancer Panel Library Preparation kits and
click Next.
4
On the Assay Parameters screen, do the following:
a In the Unique Plate Name field, type a name for the
sample plate.
b In the Index Reads field, select the number of indexes
to run for the samples on this plate: 0, 1, or 2.
c Click Next.
5
On the Plate Samples screen, click the Table or Plate tab.
You can enter information for the wells in your plate
using either view.
6
For each well that contains a sample, do the following:
a Enter a unique sample ID.
b Specify what index adapter you intend use for each
index read.
c Enter the name of the manifest file Illumina provided
for your assay or control, leaving off the .txt file
extension part of the file name.
Part # 15037154 Rev. D
If you want to capture more detailed information
about the plate, enter a sample name, project, and
description.
WARNING
The sample plate file must contain the *.amp28.plt file
extension.
Create a Sample Sheet
This section provides instructions for creating a sample sheet
for the analysis of MiSeq®, HiSeq®, HiScanSQ™, Genome
Analyzer™, or NextSeq™ sequencing data.
Create a MiSeq-Compatible Sample Sheet
1
On the IEM main screen, click Create Sample Sheet.
2
On the Instrument Selection screen, select MiSeq and click
Next.
3
On the MiSeq Application Selection screen, select the
desired category and application for your kit, and then
click Next.
For TruSeq Amplicon products, the following categories
and applications are supported:
Category
Application
Targeted Resequencing
TruSeq Amplicon
Other
FASTQ Only
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Create TruSeq Custom Amplicon or TruSeq Amplicon Cancer Panel Sample Plates and Sample Sheets with IEM
4
On the Workflow Parameters screen, do the following:
a In the Reagent Cartridge Barcode field, enter the
barcode number of the MiSeq reagent cartridge.
b
c
d
e
f
g
h
In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2.
Type an experiment name, investigator name, and
description.
Select the date.
For the FASTQ Only application, select a Paired End
or Single Read sequencing run. The TruSeq Amplicon
application only allows the Paired End option.
Select the number of cycles for each read in your
sequencing run, plus 1.
Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
If you are creating a sample sheet for the TruSeq
Amplicon application for TruSeq Amplicon - Cancer
Panel, make sure that Use Somatic Variant Caller is
checked. It is recommended for use with TruSeq
Amplicon - Cancer Panel Library Preparation.
Click Next.
5
On the Sample Selection screen, click Select Plate and
navigate to a sample plate you created previously. If you
have not yet created a sample plate, you can do so now by
clicking New Plate.
6
Click Select All to include all wells in this sequencing run
or highlight the wells you want to include in this
sequencing run.
7
Click Add Selected Samples.
8
[Optional] Click Add Blank Row to add rows and
manually enter the sample information.
9
Type a sample name, sample project, and description for
each sample.
Create a HiSeq-, HiScanSQ-, or Genome AnalyzerCompatible Sample Sheet
1
On the IEM main screen, click Create Sample Sheet.
2
On the Instrument Selection screen, select HiSeq
2500/2000/1000, HiScanSQ, GA and click Next.
3
On the HiSeq Application Selection screen, select the
HiSeq FASTQ Only application and then click Next.
4
On the Workflow Parameters screen, do the following:
a In the Reagent Kit Barcode field, enter the reagent kit
ID from the label of either box 1 or box 2 of the SBS
kit.
b From the Sample Prep Kit drop-down menu, select
TruSeq Amplicon.
c In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2.
d Type an experiment name, investigator name, and
description.
e Select the date from the calendar.
f Select a Paired End or Single Read sequencing run.
g Select the number of cycles for each read in your
sequencing run, plus 1.
If you are performing a paired-end sequencing run,
Illumina recommends performing the same number of
cycles in both reads.
h Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
i
Click Next.
5
On the Sample Selection screen, click Select Plate and
navigate to the sample plate you created previously. If you
have not yet created a sample plate, you can do so now by
clicking New Plate.
6
For each lane you are using in the flow cell, do the
following:
a Click the lane number: 1 through 8 on the sample
sheet area of the screen.
b Click Select All to include all wells in this sequencing
run or highlight the wells you want to include in this
sequencing run.
c Click Add Selected Samples.
d [Optional] Click Add Blank Row to add rows and
manually enter the sample information.
7
Type a sample name, sample reference, sample project,
and description for each sample in each lane.
8
When the wells and samples for every lane in the flow
cell have been defined, click Finish and save the sample
sheet file in the desired folder.
10 If you are creating a sample sheet for the TruSeq
Amplicon application, do the following:
a Enter the name of the Illumina provided Manifest file
for your assay or control, leaving off the .txt file
extension part of the file name.
b Select where the FASTA reference files are saved from
the Genome Folder drop-down menu.
11 Click Finish and save the sample sheet file.
12 When prompted, click Yes if you want to review the
sample sheet in Microsoft Excel or No to exit the sample
sheet wizard without reviewing the sample sheet.
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Part # 15037154 Rev. D
Create TruSeq Custom Amplicon or TruSeq Amplicon Cancer Panel Sample Plates and Sample Sheets with IEM
9
When prompted, click Yes if you want to review the
sample sheet in Microsoft Excel or No to exit the sample
sheet wizard without reviewing the sample sheet.
8
When prompted, click Yes if you want to review the
sample sheet in Microsoft Excel or No to exit the sample
sheet wizard without reviewing the sample sheet.
Create a NextSeq-Compatible Sample Sheet
Technical Assistance
1
On the IEM main screen, click Create Sample Sheet.
2
On the Instrument Selection screen, select NextSeq and
click Next.
For questions, see Illumina Experiment Manager on
www.illumina.com. If you do not find the information you
need there, contact Illumina Technical Support by email or
phone.
3
On the NextSeq Application Selection screen, select the
NextSeq FASTQ Only application for the GenerateFASTQ
workflow, and then click Next.
4
On the Workflow Parameters screen, do the following:
a In the Reagent Kit Barcode field, enter the reagent kit
ID from the label of either box 1 or box 2 of the SBS
kit.
b From the Sample Prep Kit drop-down menu, select
TruSeq Amplicon.
c In the Index Reads field, select .
d In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2.
e Type an experiment name, investigator name, and
description.
f Select the date from the calendar.
g Select a Paired End or Single Read sequencing run.
h Select the number of cycles for each read in your
sequencing run, plus 1.
If you are performing a paired-end sequencing run,
Illumina recommends performing the same number of
cycles in both reads.
i
Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
j
Click Next.
5
On the Sample Selection screen, click Select Plate and
navigate to the sample plate you created previously. If you
have not yet created a sample plate, you can do so now by
clicking New Plate.
a Click Select All to include all wells in this sequencing
run or highlight the wells you want to include in this
sequencing run.
b Click Add Selected Samples.
c [Optional] Click Add Blank Row to add rows and
manually enter the sample information.
6
Type a sample name, sample reference, sample project,
and description for each sample.
7
When the wells and samples have been defined, click
Finish and save the sample sheet file in the desired folder.
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SeqMonitor, Solexa, TruGenome, TruSeq, TruSight, Understand Your
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the property of their respective owners.
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