Journal: bioRxiv

Article Title: Commercial ChIP-Seq library preparation kits performed differently for different classes of protein targets

doi: 10.1101/2022.04.19.488832

Figure Lengend Snippet: Experimental design. Diagram outlining the experimental design for comparing the Bioo NEXTflex, Diagenode MicroPlex, Roche KAPA HyperPrep, and New England BioLabs NEBNext Ultra II ChIP-Seq library preparation protocols. Two independent ChIP-Seq experiments (sets 1 and 2) were carried out to assess H3K4me3 and H3K27me3 libraries, and three independent ChIP-Seq experiments (sets 1-3) were performed to evaluate CTCF libraries. For H3K4me3 and H3K27me3, six different amounts of input DNA (10, 5, and 1 ng and 500, 250, and 100 pg), were used for library construction; however, due to low recovery of CTCF ChIP DNA, only a single DNA input was used for library construction. The number of amplification cycles for each protocol followed the manufacturers’ recommendations based on the amount of input DNA.

Article Snippet: ChIP libraries were prepared using the NEXTflex ChIP-Seq Kit (Bioo Scientific, now PerkinElmer) following the manufacturer’s protocol.

Techniques: ChIP-sequencing, Amplification

Journal: bioRxiv

Article Title: Commercial ChIP-Seq library preparation kits performed differently for different classes of protein targets

doi: 10.1101/2022.04.19.488832

Figure Lengend Snippet: Performance of protocols for CTCF ChIP-Seq. Libraries for CTCF sets 1-3 are presented. A. Number of peaks called in each library. B. Percentage of peaks with CTCF motifs within 100 bp of peak summits. C. Histogram of distance between peak summit and CTCF motif.

Article Snippet: ChIP libraries were prepared using the NEXTflex ChIP-Seq Kit (Bioo Scientific, now PerkinElmer) following the manufacturer’s protocol.

Techniques: ChIP-sequencing