• Incubate the samples open on the magnetic stand at RT 15 min to dry residual ETOH.
• Remove samples from magnetic stand and resuspend the dry pellet in each sample with
32.5μl of Resuspension Buffer. Gently pipette up and down 10Â to mix.
• Incubate samples at RT for 2 min.
• Place the samples on the magnetic stand at RT for at least 5 min making sure liquid
clears.
• Transfer 30μl of clear supernatant from each sample to the corresponding 1.5 mL
non-sticky Sarstedt microcentrifuge tube. Some residual liquid may remain in each
sample.
Amplified libraries can be stored at À20
C for up to 7 days
9. Validate Library
• Determine the concentration of each amplified library using the Nanodrop.
• Perform QC of the amplified library by running 1μl of each sample on the Agilent
4200 Bioanalyzer using the Agilent DNA 1000 Chip.
• The final product should be a band at approximately 280 bp for a single read library.
• Calculate the nM concentration of each library.
Example Protocol: TruSeq ChIP Library Prep Kit (Illumina)
• Verify the size distribution of each ChIP DNA sample by running a 2μl aliquot on
Agilent High Sensitivity DNA chip using an Agilent Technologies TapeStation.
• Quantify 1μl of each ChIP DNA sample using a Qubit 1Â dsDNA HS Assay Kit
(invitrogen: Q33231).
• Illumina recommends normalizing the ChIP DNA samples to a final volume of 50μl at
100–200 pg/μl.
• Remove the AMPure XP beads from storage and let stand for at least 30 min to bring
them to room temperature.
• Pre-heat the thermal cycler to 30
C.
• Choose the thermal cycler pre-heat lid option and set to 100
C.
• Freshly prepare 70% ethanol (with sterile Distilled Water (DNase/Rnase Free).
• Remove the A-Tailing Mix from À15
C to À25
C storage and thaw at room
temperature.
1. Polish ChIP DNA ends
• Use 50μl ChIP sample.
• For Input samples, dilute 10 ng into 50μl total volume (ddH 2 O).
200
Appendix
• Remove samples from magnetic stand and resuspend the dry pellet in each sample with
32.5μl of Resuspension Buffer. Gently pipette up and down 10Â to mix.
• Incubate samples at RT for 2 min.
• Place the samples on the magnetic stand at RT for at least 5 min making sure liquid
clears.
• Transfer 30μl of clear supernatant from each sample to the corresponding 1.5 mL
non-sticky Sarstedt microcentrifuge tube. Some residual liquid may remain in each
sample.
Amplified libraries can be stored at À20
C for up to 7 days
9. Validate Library
• Determine the concentration of each amplified library using the Nanodrop.
• Perform QC of the amplified library by running 1μl of each sample on the Agilent
4200 Bioanalyzer using the Agilent DNA 1000 Chip.
• The final product should be a band at approximately 280 bp for a single read library.
• Calculate the nM concentration of each library.
Example Protocol: TruSeq ChIP Library Prep Kit (Illumina)
• Verify the size distribution of each ChIP DNA sample by running a 2μl aliquot on
Agilent High Sensitivity DNA chip using an Agilent Technologies TapeStation.
• Quantify 1μl of each ChIP DNA sample using a Qubit 1Â dsDNA HS Assay Kit
(invitrogen: Q33231).
• Illumina recommends normalizing the ChIP DNA samples to a final volume of 50μl at
100–200 pg/μl.
• Remove the AMPure XP beads from storage and let stand for at least 30 min to bring
them to room temperature.
• Pre-heat the thermal cycler to 30
C.
• Choose the thermal cycler pre-heat lid option and set to 100
C.
• Freshly prepare 70% ethanol (with sterile Distilled Water (DNase/Rnase Free).
• Remove the A-Tailing Mix from À15
C to À25
C storage and thaw at room
temperature.
1. Polish ChIP DNA ends
• Use 50μl ChIP sample.
• For Input samples, dilute 10 ng into 50μl total volume (ddH 2 O).
200
Appendix