Create TruSight HLA Sample Plates and Sample Sheets with IEM Quick Reference Card (15069713 B)

Create TruSight HLA Sample Plates and Sample Sheets with IEM Quick Reference Card (15069713 B)
Create TruSight HLA 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 TruSight® HLA 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.
Create a Sample Plate
b
8
Open the IEM software.
2
On the IEM main screen, select Create Sample Plate.
3
From the Sample Prep Kit list, select a Nextera XT v2 set
(A, B, C, or D), and then select 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 2.
c Select Next.
5
On the Plate Samples screen, select the Table tab.
6
For each well that contains a sample, do the following:
a Enter a unique sample ID and an identical sample
name.
The required sample name format is
DNASource-HLAGeneTarget-DateOfExperiment. There
is a 20 character limit. Use only numbers and letters
with a dash between each identifier. For example,
Sample1-DQB1-022515.
b Select Apply Default Index Layout or specify what
index adapter you intend to use for each index.
c If you want to capture more detailed information
about the plate, enter a sample project and
description.
7
[Optional] Select the Plate Graphic tab to view the sample
ID 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.
Part # 15069713 Rev. B
Select Finish and save the sample plate file.
WARNING
The sample plate file must contain the *.nexenr28.plt file
extension.
Create a MiSeq-Compatible Sample Sheet
NOTE
A sample plate is not required to generate a sample sheet,
but can be useful for organizing samples.
1
You can paste the image into any graphics-enabled
program, such as Paint, Microsoft PowerPoint,
Microsoft Word, and Adobe Photoshop.
If you want to print an image of your sample plate,
select Print on the Plate Graphics tab.
NOTE
If you combined more than 1 index kit, create a sample sheet
for each kit used and manually combine each sample sheet
into a master sample sheet as described in step 8.
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
Other category, and then select the TruSight HLA
application, and then select Next.
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 From the Sample Prep Kit drop-down menu, select a
Nextera XT v2 set (A, B, C, or D).
c The Index Reads field is automatically set to 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 251.
h Set the Quality Score Trim to 1.
i
Check the Use Adapter Trimming checkbox.
j
Select Next.
5
Add sample information to the sample sheet. Choose from
the following:
• To import an existing sample plate, proceed to step 6.
• To add new sample information, proceed to step 7.
6
Import an existing sample plate.
a On the Sample Selections screen, clear the Maximize
checkbox to display the Sample Plate area.
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Create TruSight HLA Sample Plates and Sample Sheets with IEM
b
c
d
e
f
Select Select Plate and navigate to a sample plate you
created previously.
Select Select All to include all wells in this sequencing
run or highlight the wells you want to include in this
sequencing run.
Select Add Selected Samples.
Select Finish and save the sample sheet file.
[Optional] To combine multiple sample sheets, see
step 8.
7
Add new sample information.
a On the Sample Selection screen, select Add Blank
Row to add rows and manually enter the sample
information.
b Type a unique Sample ID and an identical Sample
Name for each sample.
The required sample name format is
DNASource-HLAGeneTarget-DateOfExperiment. There
is a 20 character limit. Use only numbers and letters
with a dash between each identifier. For example,
Sample1-DQB1-022515.
c Select the Index1 (I7) and Index2 (I5) indexes from
the drop-down list in each cell.
d Select Finish and save the sample sheet file.
e [Optional] To combine multiple sample sheets, see
step 8.
8
[Optional] If there are multiple sample sheets, use Excel to
combine the sample data rows into a single master
sample sheet.
a Open each sample sheet in Excel.
b Choose a sample sheet to act as the master sample
sheet. All other sample sheets are secondary sample
sheets.
c In a secondary sample sheet, copy all the sample data
rows below the header row in the [DATA] section.
d In the master sample sheet, paste the copied rows
below the last sample data row in the [DATA] section.
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,
Powered by Illumina, SeqMonitor, SureMDA, TruGenome, TruSeq,
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.
NOTE
In the secondary sample sheet, do not copy the
header rows such as Sample_ID or Sample_Name.
In the master data sheet, do not paste over the
original sample rows or add blank rows.
e
f
Repeat the process for each secondary sample sheet.
Save the master sample sheet file.
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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Part # 15069713 Rev. B
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