title: GSM4407559: NG-Capture C siCTL rep2; Homo sapiens; OTHER
library_construction_protocol: The experiments were performed as previously described in (Davies et al., 2016b). Briefly, 3C libraries were generated using 900 U of the Dpn II restriction enzyme (NEB: R0543M) for 11 million cells and 720 U of the T4 DNA HC ligase (Life Technologies: EL0013). 3C libraries were sonicated (Bioruptor® Pico sonication device; 5 cycles; 30s ON/OFF). Samples were indexed to allow multiplexing using Illumina paired-end sequencing adaptors (NEB: E6040, E7335) and the Herculase II polymerase (Agilent: 600677). Oligonucleotide capture was then performed using 70-mer biotinylated DNA oligonucleotides designed at each of the studied target gene promoters (http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi). The hybridization reaction was performed using Nimblegen SeqCap EZ kits (Roche: 05634261001, 07145594001, 06777287001). After a 72h hybridization step, streptavidin bead pulldown (Invitrogen: 65305) was performed, followed by multiple washes (according to SeqCap EZ SR user's guide) followed by PCR amplification of the captured material. A second capture step was performed as above. Samples were indexed to allow multiplexing using Illumina paired-end sequencing adaptors (NEB: E6040, E7335) and the Herculase II polymerase (Agilent: 600677).
attributes.tag: GEO Accession
attributes.value: GSM4407559