Nature research paper: The little skate genome and the evolutionary emergence of wing-like fins
Stg.30 pectoral fin buds, each consisting of ten fins, were fixed in a final concentration of 1% PFA for 10 min at room temperature. Fixation was stopped by placing the samples on ice and by adding 1 M glycine up to a concentration of 0.125 M. The quenched PFA solution was then removed and the tissue was resuspended in ice-cold Hi-C Lysis Buffer . The lysis was helped with a Dounce Homogenizer Pestle A on ice .
A total of 130 µl was used for DNA sonication in a M220 Covaris Sonicator . After sonication, DNA was size-selected using AMPure XP beads . In brief, in a first selection, 0.6× bead mix was used and the supernatant was recovered. In the second selection, 1.2× bead mix was used and the bead fraction was recovered. Size-selected DNA was resuspended in 50 µl of TLE and then processed for end repair. End repair was performed by adding 20 µl of the end repair mix , 2.
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