Wed, 11/27/2013 at 8:59 AM
Customer calls and says he wants AccuraScience to help re-analyze a ChIP-seq dataset from a published study deposited to GEO. AccuraScience LB looks at GEO and discovers that the dataset does not include an IgG control. Customer 2013.11.26.14.38 acknowledges this and forwards the original article the dataset was associated with, and asks AccuraScience for opinion as of whether IgG control is essential.
Wed, 11/27/2013 at 11:11 AM
AccuraScience LB: They did not have either IgG or input DNA control. Considering how recently this study was published (2012) and which journal it was published in (Blood), this is somewhat out of the ordinary. It is still possible to do the ChIP-seq analysis, using the background level of the same dataset as control - some of the earlier ChIP-seq studies were done this way. Without IgG or input DNA controls, higher level of false positive signals should be expected. It is hard to say how bad this can be, because the success of a ChIP-seq study depends on many factors, e.g., quality of the antibody, skills of the person preparing the samples, and the skills of the person who operates the sequencing machine.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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