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Create TruSeq or TruSight Amplicon Sample Plates and
Sample Sheets with IEM
FOR RESEARCH USE ONLY
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, select 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,
select Print... on the Plate Graphics tab.
This quick reference card describes how to use the Illumina®
Experiment Manager (IEM) to create a TruSeq® Custom
Amplicon, TruSeq Amplicon - Cancer Panel, or TruSight™
DNA Amplicon sample plate, and create and edit sample
sheets compatible with your Illumina sequencing system and
analysis software.
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). New or less experienced users are advised to read
the guide before using this quick reference card.
8
Click Finish and save the sample plate file.
WARNING
The sample plate file must contain the *.amp28.plt file
extension.
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, select 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
then select Next.
4
5
6
7
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.
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, select Create Sample Sheet.
2
On the Instrument Selection screen, select MiSeq, and
then select Next.
3
On the MiSeq Application Selection screen, select the
desired category and application for your kit, and then
select Next.
For TruSeq Amplicon products, the following categories
and applications are supported:
On the Plate Samples screen, select the Table or Plate tab.
You can enter information for the wells in your plate
using either view.
For each well that contains a sample, do the following:
a Enter a unique sample ID.
b Specify what index adapter you intend to 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.
d If you want to capture more detailed information
about the plate, enter a sample name, project, and
description.
[Optional] Click the Plate Graphic tab to view the sample
Part # 15037154 Rev. E
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Category
Application
Targeted Resequencing
TruSeq Amplicon
Other
FASTQ Only
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
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.
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Create TruSeq or TruSight Amplicon Sample Plates and Sample Sheets with IEM
d
e
f
g
h
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, select 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
selecting 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.
HiSeq FASTQ Only application, and then select Next.
5
On the Workflow Parameters screen, do the following:
a In the Reagent Kit Barcode field, enter the reagent kit
ID from the label of 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 Select or clear the Workflow-Specific Settings
checkboxes, as desired.
i
Click Next.
6
On the Sample Selection screen, select 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
selecting New Plate.
7
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.
8
Type a sample name, sample reference, sample project,
and description for each sample in each lane.
9
When the wells and samples for every lane in the flow
cell have been defined, select 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, select 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 HiSeq-, HiScanSQ-, or Genome AnalyzerCompatible Sample Sheet
1
On the IEM main screen, select Create Sample Sheet.
10 When prompted, select 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.
2
On the Instrument Selection screen, select HiSeq,
HiScanSQ, GA, and then select Next.
Create a NextSeq-Compatible Sample Sheet
3
On second the Instrument Selection screen, select HiSeq
3000, 4000HiSeq 1500, 2500HiSeq 1000, 2000HiScanSQ,
or Genome Analyzer, and then select Next.
4
1
On the IEM main screen, select Create Sample Sheet.
2
On the Instrument Selection screen, select NextSeq, and
then select Next.
On the HiSeq Application Selection screen, select the
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Part # 15037154 Rev. E
Create TruSeq or TruSight Amplicon Sample Plates and Sample Sheets with IEM
3
On the NextSeq Application Selection screen, select the
NextSeq FASTQ Only application for the GenerateFASTQ
workflow, and then select 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, select 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
selecting 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, select
Finish and save the sample sheet file in the desired folder.
8
When prompted, select 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.
Copyright and Trademarks
© 2015 Illumina, Inc. All rights reserved.
Illumina, 24sure, BaseSpace, BeadArray, BlueFish, BlueFuse, BlueGnome,
cBot, CSPro, CytoChip, DesignStudio, Epicentre, GAIIx, Genetic Energy,
Genome Analyzer, GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X,
Infinium, iScan, iSelect, MiSeq, NeoPrep, Nextera, NextBio, NextSeq,
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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 U.S. and/or other countries. All other
names, logos, and other trademarks are the property of their respective
owners.
Technical Assistance
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.
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