Journal: Methods in enzymology

Article Title: Genomic mapping of DNA-repair reaction intermediates in living cells with engineered DNA structure-trap proteins

doi: 10.1016/bs.mie.2021.09.015

Figure Lengend Snippet: SsEND-seq mapping of 3ʹ-ssDNA-ends in E. coli. (A) Diagram of SsEND-seq. ExID-FLAG-bound 3ʹ-ssDNA ends are immunoprecipitated with anti-FLAG antibody, followed by strand-specific library preparation using the Takara DNA SMART ChIP-Seq Kit, in which 5ʹ and 3ʹ ends of ssDNA fragments are tagged with known adapter sequences, then sequenced and a genomic map of recurrent 3ʹ-ssDNA ends is made. (B) SsEND-seq detects asymmetrical peaks. SsEND-seq reads are mapped to the top (TOP, orange) or bottom (BTM, purple) strand, and form different asymmetrical peaks in which summits indicate recurrent DNA 3ʹ ssDNA termini that ExID traps. (C) SsEND-seq detects peaks of predicted asymmetry and strandedness (Liu et al. (n.d.)). Heatmaps of SsEND-seq signals around peak summits of ~220 recurrent 3ʹ-ssDNA end sites. The signals were normalized by Reads Per Kilobase per Million mapped reads (RPKM), and sorted according to signal intensity. Signals are displayed along ±300-nt regions around and centered along the peak summits.

Article Snippet: 3 Prepare library with the Takara DNA SMART ChIP-Seq Kit according to its user manual.

Techniques: Immunoprecipitation, ChIP-sequencing

Journal: STAR Protocols

Article Title: Isolation of nuclei from frozen human subcutaneous adipose tissue for full-length single-nuclei transcriptional profiling

doi: 10.1016/j.xpro.2023.102054

Figure Lengend Snippet:

Article Snippet: SMART-Seq® ICELL8® Application Kit – 5 Chip , TakaraBio USA , 640221.

Techniques: Recombinant, Imaging, Protease Inhibitor, dsDNA Assay, Cell Counting, Electron Microscopy