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For this reason, several studies have argued for studying combinatorial interactions among TFs using ChIP-based technologies [16], [17].
Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years.
Global level profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years, from hybridization with spotted or tiling microarray (ChIP-chip) [ 1- 4], to SAGE-like tags (ChIP-SAGE) [ 5] or pair-end tag sequencing (ChIP-PET) [ 6], to current massively parallel sequencing (ChIP-seq) [ 7- 10].
The development of molecular inversion probes (MIPs) and the use of chip-based technologies for massively parallel capture of specific genomic targets is limited by representational and allelic bias and remains costly and time consuming [ 2, 3].
The development of chip-based technologies using non-sandwich detection formats are of considerable interest, because of the reduced complexity and shortened measurement time.
We systematically compared different ChIP-based technologies as well as different breast cancer cells.
However, ChIP-based technologies have inherent resolution limit given the fragmentation limit of chromatin DNA [ 3].
We compared the different ChIP-based technologies as well as different breast cancer cells.
We also found that there are ~40% common TFs regulated by ERα among three different ChIP-based technologies.
We then comprehensively characterize the SOX2 response program by an integrated analysis using several advanced genomic technologies including ChIP-seq, microarray profiling, and microRNA sequencing.
Currently, chip-based technology is the most high-throughput SNP genotyping platform.
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