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Adapter ligation

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Illumina adapter ligation is a core step in the next-generation sequencing (NGS) library preparation process. It involves the attachment of universal adapter sequences to the DNA or RNA fragments being sequenced. These adapters serve as binding sites for sequencing primers and enable the fragments to be amplified and sequenced on Illumina platforms.

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Illumina adapters (41 citations) TruSeq adapter ligation (3 citations) Paired-end adapter ligation (2 citations)

2 protocols using adapter ligation

1

Profiling Chromatin Interactions in T Cells

Cited 1 time
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The detailed procedure of the modified Hi-C protocol (called meHi-C) was described in another manuscript31 . We applied the technique to naïve CD4+ T cells which were crossed linked with formaldehyde. Cells were lysed and digested with CviQ I + CviA II + Bfa I for 20 min. The Hi-C samples were processed following the in situ Hi-C protocol30 (link) with modifications briefly described as follows: DNA ends were marked by biotin-14-dATP with Klenow (large) for 1 h at 37 °C. Blunt-end DNA fragments were ligated with T4 DNA Ligase overnight at 16 °C. DNA was then reverse cross-linked and purified by phenol–chloroform extraction. Biotin was removed from unligated DNA-ends by T4 DNA polymerase for 2 h at 12 °C. DNA was purified by phenol-chloroform and sheared to 300–500 bp by sonication followed by DNA-end repair and addition of “A”46 (link). Biotin-labeled DNA was pull-downed by streptavidin beads followed by Illumina adapter ligation and PCR amplification. Hi-C experiments were done with n = 2 independent experiments for Mll4 KO naïve CD4+ T cells and n = 3 independent experiments for the control cells.
Placek K., Hu G., Cui K., Zhang D., Ding Y., Lee J.E., Jang Y., Wang C., Konkel J.E., Song J., Liu C., Ge K., Chen W, & Zhao K. (2017). MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping. Nature immunology, 18(9), 1035-1045.
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2

Profiling Chromatin Interactions in T Cells

Cited 1 time
Check if the same lab product or an alternative is used in the 5 most similar protocols
The detailed procedure of the modified Hi-C protocol (called meHi-C) was described in another manuscript31 . We applied the technique to naïve CD4+ T cells which were crossed linked with formaldehyde. Cells were lysed and digested with CviQ I + CviA II + Bfa I for 20 min. The Hi-C samples were processed following the in situ Hi-C protocol30 (link) with modifications briefly described as follows: DNA ends were marked by biotin-14-dATP with Klenow (large) for 1 h at 37 °C. Blunt-end DNA fragments were ligated with T4 DNA Ligase overnight at 16 °C. DNA was then reverse cross-linked and purified by phenol–chloroform extraction. Biotin was removed from unligated DNA-ends by T4 DNA polymerase for 2 h at 12 °C. DNA was purified by phenol-chloroform and sheared to 300–500 bp by sonication followed by DNA-end repair and addition of “A”46 (link). Biotin-labeled DNA was pull-downed by streptavidin beads followed by Illumina adapter ligation and PCR amplification. Hi-C experiments were done with n = 2 independent experiments for Mll4 KO naïve CD4+ T cells and n = 3 independent experiments for the control cells.
Placek K., Hu G., Cui K., Zhang D., Ding Y., Lee J.E., Jang Y., Wang C., Konkel J.E., Song J., Liu C., Ge K., Chen W, & Zhao K. (2017). MLL4 prepares the enhancer landscape for Foxp3 induction via chromatin looping. Nature immunology, 18(9), 1035-1045.
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