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PCR products were treated at 22°C for 30 min with T4 DNA polymerase in the presence of dTTP, using the following reaction setup: 0.2 pmol purified PCR product, 2 µL 10× buffer 2 (NEB), 2 µL dATP (25 mM), 1 µL DTT (100 mM), 2 µL 10× BSA (10 mg/mL; NEB), 1 U T4 DNA polymerase (NEB) in a volume of 20 µL (filled up with ddH2O).
To obtain blunt ended fragments, 45 µl of H2O, 10 µl of T4 DNA ligase buffer with 10 mM ATP (New England Biolabs (NEB)), 4 µl 10 mM dNTP mix (Invitrogen), 5 µl T4 DNA polymerase (NEB), 1 µl Klenow DNA polymerase (NEB), and 4 µl T4 polynucleotide kinase (NEB) were added to 5 µg of fragmented DNA in 30 µl EB (Qiagen) and incubated for 30 min at 20°C.
PCR amplifications (50 µl) comprised 19 µl of end-repaired-linker-ligated aurochs DNA, 1× Phusion® High-Fidelity DNA polymerase buffer (NEB), 1 µl of forward primer, 1 µl of reverse primer (Illumina, catalogue no. FC-102-1003), 250 nM of each dNTP (Invitrogen) and 1 unit Phusion® High-Fidelity DNA polymerase (NEB).
Ligation reactions (in 50 µl volumes) involved incubation of 19 µl of phosphorylated blunt-ended aurochs DNA extracts, with a 3'-dATP overhang, with 1× DNA ligase buffer (NEB), 1 µl of the proprietary Illumina GA single-read genomic adaptors (Illumina, catalogue no. FC-102-1003) and 10 units T4 DNA ligase (Invitrogen).
The membrane was blotted with a mouse monoclonal MalE antibody (NEB) (1: 3000) overnight at 4°C.
The labelling reaction included 1× exo- reaction buffer (NEB), 1 μL Starfire Universal template oligonucleotide (IDT) and 0.5 pmol Starfire oligonucleotide probe.
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Each plasmid was transformed into NEB DH5α chemically competent cells (NEB).
CIP treatment was performed by incubating 20 µg "total RNA" in 20 µl of 1X NEB buffer #3 containing 20U CIP (NEB) for 30 min at 37°C, followed by 30 min at 50°C.
Loading control antibodies were specific for: β-actin (rabbit mAb, #4970; NEB), STAT3 (rabbit, #4904; NEB), p42/44 MAPK (mouse mAb, #4696; NEB), and p38α MAPK (mouse mAb, #9217; NEB).
In prophase, when cyclin B activity reaches a high threshold, chromosome condensation occurs followed by Nuclear Envelope Breakdown (NEB) [1].
T4 PNK (NEB, #M0201 V) and CIP (NEB, #M0290 V) were used to modify the terminals of DNA fragments.
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