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
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Column
Record Details
Step Data (Master Step Fields)
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
Record Details
Step Data (Master Step Fields)
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
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
Record Details
Step Data (Master Step Fields)
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
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
Record Details
Step Data (Master Step Fields)
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
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
Record Details
Step Data (Master Step Fields)
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
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
Placement = Enabled
Defaults
Sample Grouping = Group by Containers
Well Sort Order = Row
Record Details
Step Data (Master Step Fields)
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
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
Record Details
Step Data (Master Step Fields)
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
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
Well
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
Derived Sample
Infinium Kit Name
Text
Read Only
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.
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
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
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.
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
Step File Placeholders
Log - Automatically attached
Sample Table
Sample Display Default = Collapse
Well Sort Order = Row
Table Columns - Global Fields
Field Name
Field Type
Options
Additional Options and Dropdown Items
Infinium HD Methylation Kits
Text
Required Field
Read Only
Default = Infinium MethylationEPIC Kit
Field Name
Field Type
Options
Additional Options and Dropdown Items
1X TE (mL)
Numeric
Read Only
1X TE for A1 (uL)
Numeric
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
Denature DNA instruction Notes
Multiline Text
Field Name
Field Type
Options
Additional Options and Dropdown Items
Instruction Notes
Multiline Text
Read Only
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
