Illumina TruSeq ChIP Library Prep Size Selection

[kate0007]

I am using the Illumina TruSeq ChIP Library prep kit to generate a library following chromatin immunoprecipitation. I will then sequence 100 bp, paired-end reads on the Illumina HiSeq platform. Before adapter ligation, most of my DNA fragments had a length of 200-250 bp.

What size should I cut out and recover following the adaptor ligation and PCR amplification? Thank you.

[huguesparri]

Adapter total length is around 120pb. So if you want 2*100nt PE sequencing, try to cut your gel around 320-350pb to avoid redundant sequences.