prepx dna chip library prep kit  (IntegenX Inc)

Journal: Genome Research

Article Title: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins

doi: 10.1101/gr.176099.114

Figure Lengend Snippet: Effect of MCM2 deficiency on nascent strand density. ( A ) All of Chr 11 (assembly mm9) with scale and chromosome band above the tracks. (1) Wt-deficient difference for exp. 1; (2) wt-deficient difference for exp. 2; (3) UCSC gene density; (4) replication timing (FSU repli-ChIP for MEF; , FSU ENCODE group); (5) lamin B1 (NKI nuclear lamina, lamin B1 for MEF; ); (6) CpG island density; (7) H3K4me1 (LICR histone H3K4me1 for MEF; , Ren Laboratory); (8) H3K4me3 (LICR histone H3K4me3 for MEF; , Ren Laboratory); (9) CTCF (LICR TFBS CTCF for MEF; , Ren Laboratory). ( B ) Correlation coefficients between different tracks calculated using the UCSC Table Browser for Chr 11 as indicated in the figure. C shows a ∼2-kbp region from Chr 10 where (1) is wt exp. 1; (2) is MCM2-deficient exp. 1; (3) is wt exp. 2; (4) is MCM2-deficient exp. 2; and (5) is total thymic DNA for the same region (control).

Article Snippet: 2), NSCR was used to assay SNSs from ∼1 × 10 8 wt or MCM2-deficient MEFs as previously, except that libraries were prepared for NGS using IntegenX PrepX DNA ChIP Library Prep kits and sequenced on a HiSeq 2000 platform in the rapid sequencing mode.

Techniques: Control