Journal: STAR Protocols

Article Title: Protocol for the genome-wide identification of intrinsic transcription factor binding motifs by mammalian-optimized pull-down sequencing

doi: 10.1016/j.xpro.2026.104513

Figure Lengend Snippet: Library preparation Schematic diagram illustrating the major steps of library construction using the NEBNext Ultra II DNA Library Prep Kit. The workflow includes. (1) end repair and dA-tailing of fragmented genomic DNA. (2) adaptor ligation (hairpin adaptor containing dU); USER enzyme cleavage to open the adaptor, and (3) PCR enrichment with indexed primers to generate the final sequencing library.

Article Snippet: Alternatives: This protocol uses NEBNext Ultra II DNA Library Prep Kit with Sample Purification Beads (NEB #E7103S) to construct library.

Techniques: Ligation, Sequencing

Journal: Cancer Informatics

Article Title: Exon-Specific Targeted Analysis of BRCA1 and BRCA2 Mutations in Bangladeshi Breast Cancer Patients

doi: 10.1177/11769351261445625

Figure Lengend Snippet: Validating the extraction of genomic DNA and PCR amplification of the desired size in 1.5% agarose gel: (A) agarose gel after genomic DNA extraction from blood samples. Genomic DNA of 5 samples is shown here in the first, D1-D5 lanes and 100 bp DNA ladder was loaded into the first lane (designated as M), (B) agarose gel after PCR amplification by the primers targeting BRCA1 exon 4 (A1) and 16 (A2) and BRCA2 exon 18 (A3), 23 (A4), and 25 (A5). Here, M denotes 100 bp DNA marker/ladder, (C) validating the presence of a specific PCR product after purification. In the first lane, 100 bp DNA ladder is denoted by M and the purified amplicons of BRCA1 exon 4 (P1) and 16 (P2) and BRCA2 exon 18 (P3), 23 (P4) and 25 (P5) are loaded from the second-sixth lanes, and (D) Agarose gel after PCR amplification by the BRCA2 F2R2 primer targeting exon 18 for patients S1 to S8.

Article Snippet: Genomic DNA from blood samples was extracted using FavorPrepTM Blood Genomic DNA Extraction Mini Kit and the genomic DNA was purified by using Monarch Genomic DNA Purification Kit (New England Biolabs), according to the manufacturer’s protocol.

Techniques: Extraction, Amplification, Agarose Gel Electrophoresis, DNA Extraction, Marker, Purification