Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
Automations
Set Array Instrument
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing Script - iScan
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
1X TE
Lambda DNA
PicoGreen dsDNA quantification reagent
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
Well
Built-in
Placement Pattern = Row
Destination Containers
96 well plate
Lambda serial dilution instruction notes
Multiline Text
Read Only
Default =
Add 66.7 uL 1X TE to well B1.
Add 100 µl 1X TE to the remaining wells of column 1.
Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.
Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.
Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
No. of QDNA Plates
Numeric Dropdown
Presets
1
2
PicoGreen (uL)
Numeric
Read Only
Sample QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate.
Add 2 µl DNA sample to each well containing PicoGreen/1xTE
Standard QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Stock Lambda DNA (ng/uL)
Numeric
Stock Lambda DNA for A1 (uL)
Numeric
Read Only
Step File Placeholders
Log - Automatically attached
Results File - Manually uploaded
Sample Table
Enable QC Flags = Yes
Sample Display Default = Collapse
Well Sort Order = Row
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
MA1-Infinium
Supplier = Illumina
Website =
MSM-Infinium
Supplier = Illumina
Website =
NaOH
RPM-Infinium
Supplier = Illumina
Website =
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Placement Pattern = Same Shape
Destination Containers
96 well plate
Default =
Add 20 µl MA1 to each well of the MSA3 plate.
Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate
Add 4 µl 0.1N NaOH in to each sample well of the plate
Add 68 μl RPM in to each sample well of the plate.
Add 75 μl MSM in to each sample well of the plate
Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
ℹ The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Default =
Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows:
150 µl RA1. Incubate for 30 seconds. Repeat 5 times.
225 µl LX1. Incubate for 10 minutes.Repeat once.
225 µl LX2. Incubate for 10 minutes. Repeat once.
300 µl EML. Incubate for 15 minutes.
250 µl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat twice.Incubate 5 minutes.
Set the the chamber rack temperature to the temperature indicated on the SML tube.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Stain Instruction Notes
Multiline Text
Read Only
Default =
Fill the reservoir of each flow-through chamber as follows:
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes. g 250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
Wash and Coat Beadships Instruction Notes
Multiline Text
Read Only
Default =
Add 310 ml PB1 to the PB1 wash dish.
Add 310 ml XC4 to the XC4 wash dish
Master Step Name = Select Infinium Kit-Infinium HD Methylation v1.2
Step Type = No Outputs
Automations
Set Infinium HD Methylation Kit Name
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Infinium HD Methylation Kits
Text
Required Field
Read Only
Default = Infinium MethylationEPIC Kit
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 2: Quantify DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Quantify DNA-Infinium PicoGreen v1.2
Step Type = Standard QC
Measurement Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
1X TE
Lambda DNA
PicoGreen dsDNA quantification reagent
Automations
Calculate Stock Lambda DNA and PicoGreen Dilution
Trigger Location = Record Details
Trigger Style = Manual button
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement Pattern = Row
Destination Containers
96 well plate
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
1X TE (mL)
Numeric
Read Only
1X TE for A1 (uL)
Numeric
Step File Placeholders
Log - Automatically attached
Results File - Manually uploaded
Sample Table
Enable QC Flags = Yes
Sample Display Default = Collapse
Step 3: Bisulfite Conversion (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Bisulfite Conversion-Infinium v1.2
Step Type = No Outputs
Reagent Kits
EZ DNA Methylation Kit
Supplier = Zymo Research
Website =
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Cleanup Conversion Reagent Instruction Notes
Multiline Text
Read Only
Default =
Use the instructions in the Zymo EZ DNA Methylation Kit to do the following.
Clean the samples using the provided spin columns or filter plate. Wash off the remaining conversion reagent.
Centrifuge the plate at 3000–5000 × g.
Desulphonate the column or the plate with desulphonation buffer.
Incubate at room temperature for 15 minutes.
Clean the samples and wash to remove the desulphonation buffer. Repeat one time.
Add 12 µl elution buffer from 500 ng gDNA.
Centrifuge to elute at 3000–5000 × g for 5 minutes
Default =
Apply a BCD barcode label
Transfer the BCD to the plate as follows:
Midi plate: 20 µl BCD sample to each well (requires ≥ 1000 ng input in bisulfite conversion)
TCY plate: 10 µl BCD sample to each well (requires ≥ 500 ng input in bisulfite conversion
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 5: Amplify DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Amplify DNA-Infinium HD Methylation v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
MA1-Infinium
Supplier = Illumina
Automations
Validate MSA4 Plate Barcode and Set Sample Placement Information
Trigger Location = Placement
Trigger Style = Automatic upon exit
Copy Infinium Kit Name
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Placement Pattern = Same Shape
Destination Containers
96 well plate
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 6: Incubate DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Incubate DNA-Infinium v1.2
Step Type = No Outputs
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 7: Fragment DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Fragment DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
FMS-Infinium
Supplier = Illumina
Website =
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes (HD Methylation & LCG)
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Column
Step 8: Precipitate DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Precipitate DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
100% 2-propanol
PM1-Infinium
Supplier = Illumina
Website =
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
100% 2-propanol Prep Date
Date
Blue Pellet Presence
Toggle Switch
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Column
Step 9: Resuspend DNA (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Resuspend DNA-Infinium v1.2
Step Type = No Outputs
Reagent Kits
RA1-Infinium
Supplier = Illumina
Website =
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes (HD Methylation & LCG)
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Column
Protocol 2: BeadChip Processing (Infinium HD Methylation Assay Manual v1.2)
Protocol Type = Sample Prep
Next Steps Configuration
Step 1: Hybridize DNA to HD BeadChip (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Hybridize DNA to BeadChip-Infinium v1.2
Step Type = Standard
Derived Sample Generation = Fixed, 1
Naming Convention = {InputItemName}
Reagent Kits
70% EtOH
PB2-Infinium
Automations
Generate Sample Placement for Infinium BeadChip
Trigger Location = Placement
Trigger Style = Automatic upon entry
Validate BeadChip Barcode
Trigger Location = Placement
Trigger Style = Automatic upon exit
Copy Sample Information
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Placement Pattern = Row
Destination Containers
8x1 HD BeadChip
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
HD Methylation Instruction Notes
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 2: Wash BeadChip (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Wash BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
PB1-Infinium
Supplier = Illumina
Website =
Automations
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Instruction Notes
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Step 3: Extend and Stain BeadChip (Infinium HD Methylation Assay Manual v1.2)
Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
ATM-Infinium
Supplier = Illumina
Website =
EDTA
PB1-Infinium
Supplier = Illumina
Website =
RA1-Infinium
Supplier = Illumina
Website =
STM-Infinium
Supplier = Illumina
Website =
TEM-Infinium
Supplier = Illumina
Website =
XC1-Infinium
Supplier = Illumina
Website =
XC2-Infinium
Supplier = Illumina
Website =
XC3-Infinium
Supplier = Illumina
Website =
XC4-Infinium
Supplier = Illumina
Website =
Automations
Set Array Instrument
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing Script - iScan
Trigger Location = Step
Trigger Style = Automatic upon exit
ℹ The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Sample Table (Column Headers)
Record Details
Step Data (Master Step Fields)
Field Name
Field Type
Options
Additional Options and Dropdown Items
Comment
Multiline Text
Extend Instruction Notes (HD Methylation)
Multiline Text
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Infinium HTS Assay Manual v1.2
Overview
The Infinium HTS Assay Manual workflow includes the following functionality.
Default =
Add 66.7 uL 1X TE to well B1.
Add 100 µl 1X TE to the remaining wells of column 1.
Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.
Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.
Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
No. of QDNA Plates
Numeric Dropdown
Presets
1
2
3
Default = 1
PicoGreen (uL)
Numeric
Read Only
Sample QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate.
Add 2 µl DNA sample to each well containing PicoGreen/1xTE
Standard QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Stock Lambda DNA (ng/uL)
Numeric
Stock Lambda DNA for A1 (uL)
Numeric
Read Only
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Read Only
Default =
Follow the instructions in the Zymo EZ DNA Methylation
Kit to denature the genomic DNA and add conversion reagent.
Incubate DNA Instruction Notes
Multiline Text
Read Only
Default =
Incubate in a thermal cycler using the following settings for 16 cycles:
95°C for 30 seconds
50°C for 1 hour
Hold DNA at 4°C for 10 minutes in the thermal cycler until cleanup
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Read Only
Default =
Add 20 µl MA1 to each well of the plate
Transfer 4 µl DNA sample from the BCD plate to the corresponding wells of the plate
Add 4 µl 0.1N NaOH in to each sample well of the plate
Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g
Add 68 μl RPM in to each sample well of the plate
Add 75 μl MSM in to each sample well of the plate
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Read Only
Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Read Only
Default = Add 50 μl FMS to each well of the plate.
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Default = None Set
Comment
Multiline Text
Instruction Notes (HD Methylation & LCG)
Multiline Text
Read Only
Default =
Add 100 μl PM1 to each well of the plate.
Add 300 μl 100% 2-propanol to each well of the plate.
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Read Only
Default = Add 46 µl RA1 to each well of the plate
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Read Only
Default = Transfer 26 µl each sample from the plate to the appropriate section of the BeadChip.
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Read Only
Default = Fill two wash dish with 200ml PB1 each and labelled Wash 1 and Wash2
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Read Only
Default =
Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows:
150 µl RA1. Incubate for 30 seconds. Repeat 5 times.
450 μl XC1. Incubate for 10 minutes.
450 μl XC2. Incubate for 10 minutes.
200 μl TEM. Incubate for 15 minutes.
450 μl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat once.
Incubate 5 minutes.
Begin ramping the Chamber Rack temperature to the temperature indicated on the STM tube, or to 37°C if none is shown
450 μl XC3. Incubate for 1 minute. Repeat once.
Stain Instruction Notes (HD Methylation)
Multiline Text
Default =
Fill the reservoir of each flow-through chamber as follows:
250 μl STM. Incubate for 10 minutes.
450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
250 μl STM and incubate for 10 minutes.
450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
250 μl STM. Incubate for 10 minutes.
450 μl XC3 and incubate for 1 minute. Repeat once, and then wait 5 minutes.
Wash and Coat Beadships Instruction Notes
Multiline Text
Read Only
Default =
Add 310 ml PB1 to the PB1 wash dish.
Add 310 ml XC4 to the XC4 wash dish
Default =
Add 66.7 uL 1X TE to well B1.
Add 100 µl 1X TE to the remaining wells of column 1.
Transfer 133.3 µl Lambda DNA from well A1 to well B1. Pipette up and down several times to mix.
Transfer 100 µl from well B1 to well C1. Pipette up and down several times to mix.
Repeat the sequential transfer of 100 µl for wells D1, E1, F1, and G1. Do not transfer from well G1 to H1. Well H1 serves as the blank 0 ng/µl Lambda DNA.
No. of QDNA Plates
Numeric Dropdown
Presets
1
2
PicoGreen (uL)
Numeric
Read Only
Sample QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 μl PicoGreen/1xTE dilution to each sample well of the Sample QDNA plate.
Add 2 µl DNA sample to each well containing PicoGreen/1xTE
Standard QDNA Plate instruction notes
Multiline Text
Read Only
Default =
Transfer 195 µl PicoGreen/1X TE dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Transfer 2 µl stock Lambda DNA dilution from the Standard DNA plate to columns 1 and 2 of the Standard QDNA plate.
Stock Lambda DNA (ng/uL)
Numeric
Stock Lambda DNA for A1 (uL)
Numeric
Read Only
Step File Placeholders
Log - Automatically attached
Results File - Manually uploaded
Sample Table
Enable QC Flags = Yes
Sample Display Default = Collapse
Well Sort Order = Row
File Column Options
File Column Display = Show
File Attachment Method = Manual
Table Columns - Global Fields
Naming Convention = {InputItemName}
Reagent Kits
MA1-Infinium
Supplier = Illumina
Website =
MA2-Infinium
Supplier = Illumina
Website =
MSM-Infinium
Supplier = Illumina
Website =
NaOH
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Placement Pattern = Same Shape
Destination Containers
96 well plate
Default =
Add 20 µl MA1 to each well of the MSA3 plate.
Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate
Add 4 µl 0.1N NaOH in to each sample well of the plate
Add 34 μl MA2 in to each sample well of the plate.
Add 38 μl MSM in to each sample well of the plate
Vortex at 1600 rpm for 1 minute, and then pulse centrifuge at 280 × g.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
Master Step Name = Extend and Stain BeadChip-Infinium v1.2
Step Type = No Outputs
Reagent Kits
Automations
Set Array Instrument
Trigger Location = Record Details
Trigger Style = Automatic upon entry
Set Next Step - Advance
Trigger Location = Record Details
Trigger Style = Automatic upon exit
Routing Script - iScan
Trigger Location = Step
Trigger Style = Automatic upon exit
Queue/Ice Bucket
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
Naming Convention = {InputItemName}
Reagent Kits
MA1-Infinium
Supplier = Illumina
Website =
MA2-Infinium
Supplier = Illumina
Website =
NaOH
RAM-Infinium
Supplier = Illumina
Website =
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Placement Pattern = Column
Destination Containers
96 well plate
Default = Infinium XT iSelect-96 Kit
Instruction Notes
Multiline Text
Read Only
Default =
Add 20 µl MA1 to each well of the plate.
Transfer 4 µl DNA sample from the DNA plate to the corresponding wells of the plate.
Add 4 µl 0.1N NaOH in to each sample well of the plate.
Add 35 μl MA2 in to each sample well of the plate.
Add 35 μl RAM in to each sample well of the plate.
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Container
Container Name
Built-in
Container
LIMS ID (Container)
Built-in
Default = Incubate the plate in the Illumina Hybridization Oven for 20–24 hours at 37°C.
ℹ The workflow version and step version for the Array Instrument may vary depending on the version of the IPP.
Sample Table (Column Headers)
Category
Field Name
Field Type
Options
Additional Options and Dropdown Items
Derived Sample
DNA Plate Barcode
Text
Read Only
Derived Sample
Infinium Kit Name
Text
Read Only
Default =
Without allowing pipette tips to touch BeadChip surfaces, fill the reservoir of each flow-through chamber as follows:
150 µl RA1. Incubate for 30 seconds. Repeat 5 times.
225 µl LX1. Incubate for 10 minutes.Repeat once.
225 µl LX2. Incubate for 10 minutes. Repeat once.
300 µl EML. Incubate for 15 minutes.
250 µl 95% formamide/1 mM EDTA. Incubate for 1 minute. Repeat twice.Incubate 5 minutes.
Set the the chamber rack temperature to the temperature indicated on the SML tube.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Stain Instruction Notes
Multiline Text
Read Only
Default =
Fill the reservoir of each flow-through chamber as follows:
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes. g 250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl ATM. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
250 µl SML. Incubate for 10 minutes.
250 µl XC3. Incubate for 1 minute. Repeat twice.
Wait 5 minutes.
Wash and Coat Beadships Instruction Notes
Multiline Text
Read Only
Default =
Add 310 ml PB1 to the PB1 wash dish.
Add 310 ml XC4 to the XC4 wash dish
