Technical data

SureSelect

Target Enrichment System for Illumina Paired-End

Sequencing Library Protocol

Agilent Technologies

Sample Preparation (3 µg DNA

Samples)

Step 1. Shear the DNA 22

Step 2. Purify the sample using AMPure XP beads 24

Step 3. Assess quality (optional) 26

Step 4. Repair the ends 28

Step 5. Purify the sample using AMPure XP beads 29

Step 6. Adenylate the 3' end of the DNA fragments 30

Step 7. Purify the sample using AMPure XP beads 31

Step 8. Ligate the paired-end adaptor 32

Step 9. Purify the sample using AMPure XP beads 33

Step 10. Amplify the adaptor-ligated library 34

Step 11. Purify the amplified library with AMPure XP beads 37

Step 12. Assess quality and quantity 38

The sample preparation protocol is used to prepare DNA libraries for

sequencing using the Illumina paired-read platform. For each sample to be

sequenced, an individual indexed library is prepared. For an overview of

the SureSelect

target enrichment workflow, see Figure 1 on page 10.

The steps in this section differ from the Illumina protocol in the use of

the Covaris system for gDNA shearing, smaller target shear size,

elimination of size selection by gel purification, implementation of AMPure

XP beads for all purification steps, and primers used for PCR. Refer to the

Illumina protocol Preparing Samples for Multiplexed Paired-End

Sequencing (p/n1005361) or the appropriate Illumina protocol for more

information.

CAUTION

This section contains instructions for the preparation of gDNA libraries from 3 g DNA

samples. For lower input (200 ng) DNA samples, see the library preparation protocol

on page 41.