I was under the impression that CUT&RUN's benefits came primarily from reducing cell input count. But with (not so recent) improvements in ChIP such as Nano-ChIP and LinDa-Chip, the latter of which brings down cell count to 10k cells (but let's take 50k for discussion), what reasons are there to really choose one method over the other?
What are the advantages of each method now that cell counts needed are much lower for ChIP sequencing, are they both equally good or are there reasons to choose one over the other?
-Jelle
Edit1: references of LinDA and Nano-ChIP
Shankaranarayanan, Pattabhiraman, et al. "Single-tube linear DNA amplification (LinDA) for robust ChIP-seq." Nature methods 8.7 (2011): 565-567.
Adli, Mazhar, and Bradley E. Bernstein. "Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq." Nature protocols 6.10 (2011): 1656-1668.
Hi.,
By combining chromatin immunoprecipitation (ChIP) assays with sequencing, ChIP sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific antibody.Chromatin immunoprecipitation (ChIP) assays identify links between the genome and the proteome by monitoring transcription regulation through histone modification (epigenetics) or transcription factor–DNA binding interactions.Analysis of ChIP-seq data
Dear CK Gomathy, thank you for your answer, but I feel this doesn't really adress any of my questions. All the things you have mentioned can be done by Cut&Run, my question is why we would want to choose one over the other?
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