Create TruSeq DNA, RNA, or ChIP Sample Plates and Sample Sheets with IEM Quick Reference Card (15037152 E)

Create TruSeq DNA, RNA, or ChIP 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® DNA, RNA, or
ChIP 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.
7
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 If you want to capture more detailed information
about the plate, enter a sample name, project, and
description.
8
[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, 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.
9
Click Finish and save the sample plate file.
NOTE
• For TruSeq Targeted RNA Expression, see Create TruSeq
Targeted RNA Expression Sample Plates and Sample Sheets
with IEM (part # 15041979)).
• For TruSeq Synthetic Long-Read DNA sample plates and
sample sheets, see Create TruSeq Synthetic Long-Read
DNA Sample Plates and Sample Sheets with IEM (part #
15069713).
Create a Sample Plate
WARNING
The sample plate file must contain the following file
extensions:
*.tru0.plt for LT plates with no indexes
*.tru16.plt for LT plates with a single index
*.truht0.plt for HT plates with no indexes
*.truht18.plt for HT plates with a single index
*.truht28.plt for HT plates with dual indexes
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 from the
following, depending on which kit type you are using:
• TruSeq LT for TruSeq v2, LT, NeoPrep, or ChIP
samples
• TruSeq HT for TruSeq HT samples
4
Click Next.
5
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 (2
indexes option for TruSeq HT only).
c Click Next.
6
On the Plate Samples screen, select the Table or Plate tab.
You can enter information for the wells in your plate
using either view.
Part # 15037152 Rev. E
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.
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Create TruSeq DNA, RNA, or ChIP Sample Plates and Sample Sheets with IEM
For TruSeq DNA, RNA, and ChIP products, the following
categories and applications are supported:
Category
Application
Targeted Resequencing
Clone Checking
Small Genome Sequencing
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.
Metagenomics 16s rRNA
10 Click Finish and save the sample sheet file.
Resequencing
11 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.
Assembly
Plasmids
RNA Sequencing
RNA-Seq
Create a HiSeq-, HiScanSQ-, or Genome AnalyzerCompatible Sample Sheet
Other
Library QC
1
On the IEM main screen, select Create Sample Sheet.
ChIP-Seq (TruSeq LT only)
2
On the Instrument Selection screen, select HiSeq,
HiScanSQ, GA, and then select Next.
3
On second the Instrument Selection screen, select HiSeq
3000, 4000HiSeq 1500, 2500HiSeq 1000, 2000HiScanSQ,
or Genome Analyzer, and then select Next.
4
On the HiSeq Application Selection screen, select the
desired application, and then select Next. For TruSeq
DNA, RNA, and ChIP products, the following
applications and workflows are supported.
FASTQ Only
4
7
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 On the Sample Prep Kit Selection screen, select from
the following, depending on which kit type you are
using:
— TruSeq LT for TruSeq v2, LT, NeoPrep, or ChIP
kits
— TruSeq HT for TruSeq HT kits
c In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2 (2 indexes with
TruSeq HT only).
d Type an experiment name, investigator name, and
description.
e Select the date.
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, 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.
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Sample Prep
Kit Option
Application in
Analysis
Workflow
IEM
in Sample
Sheet
TruSeq LT
TruSeq HT
5
Human Genome
Resequencing
Resequencing
HiSeq FASTQ Only
GenerateFASTQ
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
from the following, depending on which kit type you
are using:
— TruSeq LT for TruSeq v2, LT, NeoPrep, or ChIP
kits
— TruSeq HT for TruSeq HT kits
c In the Index Reads field, select the number of indexes
you will run for the samples: 0, 1, or 2 (2 indexes
option with TruSeq HT only).
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.
Part # 15037152 Rev. E
Create TruSeq DNA, RNA, or ChIP Sample Plates and Sample Sheets with IEM
g
h
i
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.
Select or clear the Workflow-Specific Settings
checkboxes, as desired.
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 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 NextSeq-Compatible Sample Sheet
1
On the IEM main screen, select Create Sample Sheet.
2
On the Instrument Selection screen, select NextSeq, and
then select Next.
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
from the following, depending on which kit type you
are using:
— TruSeq LT for TruSeq v2, LT, NeoPrep, or ChIP
kits
— TruSeq HT for TruSeq HT kits
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 (2 indexes
option with TruSeq HT only).
Type an experiment name, investigator name, and
description.
Select the date from the calendar.
Select a Paired End or Single Read sequencing run.
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.
Check or uncheck the Workflow-Specific Settings
checkboxes, as desired.
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.
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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