Chromatin Immunoprecipitation:Article Title: The KH domain facilitates the substrate specificity and unwinding processivity of DDX43 helicase
Article Snippet: .. For the DNA library, 20 ng of ChIP-ed DNA was end-repaired using NEBNext Ultra II End Prep buffer and Enzyme mix, adaptor-ligated, cleaned with 0.9×AMPure beads, and size-selected using 0.4×beads. .. The size-selected DNA was then amplified using (index 3, 4, 5, 6, 7, and 8) NEBNext Multiplex Oligos for Illumina and universal primers (E7335, NEB).
Article Title: Structure-function analysis of DEAD-box helicase DDX43.
Article Snippet: 6) The DNA library was prepared using a NEBNext Ultra II DNA library prep kit (E7645, NEB) according to the manufacturer’s instructions. .. 20 ng of ChIP-ed DNA was end-repaired using NEBNext Ultra II End Prep buffer and Enzyme mix, adaptorligated, cleaned with 0.9 × AMPure beads, and size selected using 0.4 × beads. .. The size-selected DNA was then amplified using (Index 3, 4, 5, 6, 7, and 8) NEBNext Multiplex Oligos for Illumina and universal primers (E7335, NEB).
Modification:Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/ μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65 ◦C. .. After cooling for 15 min, 1.25 μl 10 pM/ μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling for 15 min, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq
Article Snippet: .. Library preparation: TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Sonication:Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/ μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65 ◦C. .. After cooling for 15 min, 1.25 μl 10 pM/ μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: Stimulation of adaptive gene amplification by origin firing under replication fork constraint
Article Snippet: Second end processing and library amplification were performed with components of the NEBNext Ultra II DNA kit (NEB E7645S) and a NEBNext Multiplex Oligos set (e.g. NEB E7335S). .. 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2 , 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling for 15 min, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: Stimulation of adaptive gene amplification by origin firing under replication fork constraint
Article Snippet: Second end processing and library amplification were performed with components of the NEBNext Ultra II DNA kit (NEB E7645S) and a NEBNext Multiplex Oligos set (e.g. NEB E7335S). .. 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2 , 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq
Article Snippet: .. Library preparation: TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Incubation:Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/ μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65 ◦C. .. After cooling for 15 min, 1.25 μl 10 pM/ μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: Stimulation of adaptive gene amplification by origin firing under replication fork constraint
Article Snippet: Second end processing and library amplification were performed with components of the NEBNext Ultra II DNA kit (NEB E7645S) and a NEBNext Multiplex Oligos set (e.g. NEB E7335S). .. 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2 , 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: KRAB zinc finger proteins ZNF587/ZNF417 protect lymphoma cells from replicative stress-induced inflammation
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells
Article Snippet: .. TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB, E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling for 15 min, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated for 30 min at room temperature.
Article Title: Stimulation of adaptive gene amplification by origin firing under replication fork constraint
Article Snippet: Second end processing and library amplification were performed with components of the NEBNext Ultra II DNA kit (NEB E7645S) and a NEBNext Multiplex Oligos set (e.g. NEB E7335S). .. 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2 , 0.5 μl NEBNext ligation enhancer and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
Article Title: Genome-wide analysis of DNA replication and DNA double-strand breaks using TrAEL-seq
Article Snippet: .. Library preparation: TrAEL-seq adaptor 2 was added using a modified NEBNext Ultra II DNA kit (NEB E7645S): 3.5 μl NEBNext Ultra II End Prep buffer, 1 μl 1 ng/μl sonicated salmon sperm DNA (this is used as a carrier), and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. .. After cooling, 1.25 μl 10 pM/μl TrAEL-seq adaptor 2, 0.5 μl NEBNext ligation enhancer, and 15 μl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature.
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