TRF2 endogenous ChIP-Seq in HT1080
TRF2-bound DNA from HT-1080 cells was quantified, and 20 ng from each sample was taken for end repair using Illumina Tru-Seq sample preparation kit. Samples were purified using PCR purification kit (Qiagen, Germany). Thereafter ‘A’ base was added to the samples 3′-end using Illumina sample preparation kit. After the end of the reaction, samples were again purified by PCR purification kit (Qiagen). Then flow-cell primer specific adapters were ligated to the ChIP DNA fragments and samples were further purified by MinElute columns. Size selection was done after adapter ligation using 2% agarose gel. Gel extraction columns (Qiagen) were used to purify DNA fragments ranging between 150 and 350 bases. These eluted samples were then purified using MinElute columns and these samples were then amplified for 18 cycles to enrich adapter-ligated DNA fragments. After PCR purification and elution the DNA was quantified using Picogreen method, and then 7 pico moles of each sample was sequenced on GAIIx (Illumina, USA) according to manufacturer's protocol.
TRF2-Chip