TruSeq ChIP Library Preparation Kit

Protocol tips

Upstream tips	Protocol tips	Downstream tips
-Remove End Repair Mix and Resuspension Buffer from -15°C to -25°C storage and thaw them at room temperature.	-5–10 ng ChIP-enriched, fragmented input DNA is recommended. -Carefully collect ChIP DNA samples to make sure that they are free of contaminants.

Upstream tips
-Remove End Repair Mix and Resuspension Buffer from -15°C to -25°C storage and thaw them at room temperature.
Protocol tips
-5–10 ng ChIP-enriched, fragmented input DNA is recommended. -Carefully collect ChIP DNA samples to make sure that they are free of contaminants.

Publication protocol

Chromatin immunoprecipitation assay experiments were performed as previously described (20, 25). The antibody for H3K4me3 was from Active Motif (Carlsbad, CA, USA). The Illumina TruSeq ChIP library preparation kit (San Diego, CA, USA) was used and sequencing was performed on an Illumina HiSeq. The reference genome (hg38) was indexed by the novoindex function of the NovoAlign package. Reads were filtered by SAM fields such as mapq, cigar, and flag and extended to 200 bp long at their 3′ end. Reads were mapped to the 1 kb promoter regions of known genes to get an integer matrix from each cell type. The read count matrices were normalized and analyzed the same way as the RNA-seq data to obtain results of differential H3K4me3.

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Manufacturer protocol

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