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The Hi-C library was prepared as described previously23 with minor modifications. Nuclear DNA was cross-linked in situ with formaldehyde, extracted, and then digested with HindIII at 37°C overnight. After digestion, the sticky ends were filled in, biotinylated, and then ligated to each other randomly to form chimeric circles. Biotinylated DNA fragments were reverse cross-linked by Proteinase K and purified by a phenol extraction, followed by a phenol/chloroform/isoamylalcohol extraction. Then, the purified DNA was sheared to a size of 300-700 bp with a Covaris S220 instrument (Covaris, Woburn, MA). The sheared DNA was end-repaired with T4 DNA polymerase. The biotin tagged ligation products were isolated with MyOne Streptavidin C1 Dynabeads (Life Technologies). Bead-bound Hi-C DNA was amplified and purified for preparing the sequencing library |
Hi-C |
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size fractionation |
PAIRED
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