1. business and industrial
2. business operations
3. business plans

Create TruSight Sample Plates and Sample Sheets with IEM
FOR RESEARCH USE ONLY
} MiSeq Manifest Repository—Select the Manage Files icon
on the MiSeq Welcome screen and upload the Manifest
file under the Manifest tab.
This quick reference card describes how to use the Illumina®
Experiment Manager (IEM) to create a TruSight™ One,
TruSight Enrichment, or TruSight Rapid Capture sample plate,
as well as create and edit sample sheets compatible with your
Illumina sequencer 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).
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.
NOTE
Note regarding biomarker patents and other patents
unique to specific uses of products.
Some genomic variants, including some nucleic acid
sequences, and their use in specific applications may be
protected by patents. Customers are advised to determine
whether they are required to obtain licenses from the party
that owns or controls such patents in order to use the
product in customer's specific application.
Workflows
NOTE
Set the default Manifest folder location on the MiSeq
Run Options screen by selecting Folder Settings.
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 TruSight
Enrichment 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 Select the appropriate Manifest from the drop-down
menu.
d If you want to capture more detailed information
about the plate, enter a sample name, project, and
description.
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.
For TruSight One and TruSight Rapid Capture, the
Enrichment workflow is the recommended analysis workflow.
Manifests
An Illumina provided manifest file is required for the
Enrichment workflow and by the analysis software to define
regions of interest (e.g., genomic coordinates of targeted
regions) and to complete the sample sheet.
To download a manifest file, go to support.illumina.com.
Select Sequencing, then Kits & Reagents. Select the sample
prep kit that you are using to open its support page. On the
support page, click the Downloads tab and select the manifest
file.
Copy the manifest file to the following locations:
} IEM Manifest Repository—Select Folder Settings on the
IEM main screen to verify location. When it is saved to
this location, the manifest is visible in the Nextera
Manifest section of the Sample Selection page.
Part # 15048138 Rev. B
1 of 4
Create TruSight Sample Plates and Sample Sheets with IEM
b
8
If you want to print an image of your sample plate,
click Print... on the Plate Graphics tab.
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
Make sure that the required sample ID, index adapters,
and Nextera Manifest are displayed. Type a sample name,
sample project, and description for each sample, as
desired
Click Finish and save the sample plate file.
WARNING
The sample plate file must contain the following file
extensions:
*.nexenr0.plt for plates with no indexes
*.nexenr18.plt for plates with a single index
*.nexenr28.plt for plates with dual indexes
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 TruSight Enrichment, TruSight One, and TruSight
Rapid Capture products, the following categories and
applications are supported:
4
Category
Application
Targeted Resequencing
Enrichment
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 From the Sample Prep Kit drop-down menu, select
TruSight Enrichment.
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.
f Select the Paired End Read Type.
g Set the number of cycles for each read to 151.
h Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
i
Click Next.
2 of 4
10 Click Finish and save the sample sheet file.
11 If the Select Included Regions dialog box appears when
selecting an Illumina provided manifest file, check which
Genomic Targets to include in the results, then click OK.
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.
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
desired application and then click Next. For TruSight
Enrichment, TruSight One, and TruSight Rapid Capture
products, the following applications and workflows are
supported.
Sample Prep Kit
TruSight One
Sequencing Panel
TruSight Rapid
Capture
TruSight Enrichment
Application
in
Analysis
Workflow
Experiment
Manager
in Sample
Sheet
HiSeq
Enrichment
Enrichment
HiSeq
FASTQ Only
GenerateFASTQ
HiSeq
Enrichment
Enrichment
Part # 15048138 Rev. B
Create TruSight Sample Plates and Sample Sheets with IEM
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
Nextera Rapid Capture Enrichment.
NOTE
The TruSight One and TruSight Rapid Capture kits
use the same analysis workflow as Nextera Rapid
Capture Enrichment.
c
d
e
f
g
h
i
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 from the calendar.
Select the Paired End Read Type.
Set the number of cycles for each read to 151 (for
HiSeq 2500 Rapid Run mode or GAIIx) or 101 (for
HiSeq 2000 or High Output mode).
Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
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
Make sure that the required sample ID, index adapters,
and Nextera Manifest are displayed. Type a sample name,
sample project, and description for each sample, as
desired
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.
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.
Create a NextSeq-Compatible Sample Sheet
NOTE
Only the TruSight Enrichment kit is supported by IEM for
the NextSeq.
1
On the IEM main screen, click Create Sample Sheet.
2
On the Instrument Selection screen, select NextSeq and
click Next.
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 In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2.
c Type an experiment name, investigator name, and
description.
d Select the date from the calendar.
e Select a Paired End or Single Read sequencing run.
f 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.
g Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
h 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
Make sure that the required sample ID, index adapters,
and Nextera Manifest are displayed. Type a sample name,
sample project, and description for each sample, as
desired
7
When the wells and samples have been defined, click
Finish and save the sample sheet file in the desired folder.
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.
3 of 4
Create TruSight Sample Plates and Sample Sheets with IEM
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.
Copyright and Trademarks
© 2013-2014 Illumina, Inc. All rights reserved.
Illumina, IlluminaDx, 24sure, BaseSpace, BeadArray, BeadXpress,
BlueFish, BlueFuse, BlueGnome, cBot, CSPro, CytoChip, DASL,
DesignStudio, Eco, GAIIx, Genetic Energy, Genome Analyzer,
GenomeStudio, GoldenGate, HiScan, HiSeq, HiSeq X, Infinium, iScan,
iSelect, MiSeq, MiSeqDx, NeoPrep, Nextera, NextSeq, NuPCR,
SeqMonitor, Solexa, TruGenome, TruSeq, TruSight, Understand Your
Genome, UYG, VeraCode, VeriSeq, the pumpkin orange color, and the
Genetic Energy streaming bases design are trademarks of Illumina, Inc. in the
U.S. and/or other countries. All other names, logos, and other trademarks are
the property of their respective owners.
4 of 4
Part # 15048138 Rev. B