title: GSM1216744: FAIRE_DL23_nt; Homo sapiens; OTHER
library_construction_protocol: library strategy: FAIRE-seq Chromatin was additionally sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by LMPCR. After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel and sequenced on SOLiD sequencer to produce 50-bp long reads. FAIRE sample was generated from 10x106 DLD1-F3 cells as described in detail (Simon et al., 2012). Briefly, cells were crosslinked in 1% formaldehyde (for 5 minutes at room temperature), lysed, collected in buffer with protease inhibitors (Roche) and dounced with a tight pestle. Nuclei were collected through centrifugation, lysed and DNA was sheared using Biorupter Sonicator. FAIRE DNA was obtained through phenol/chloroform/isoamyl alcohol and chloroform/isoamyl (SIGMA) extraction. DNA was treated with DNase-free RNase and proteinase K (Ambion), decrosslinked overnight at 65C and purified with Qiaquick PCR purification kit (Qiagen).
attributes.tag: GEO Accession
attributes.value: GSM1216744