Fri, 12/13/2013
Customer is a cancer researcher seeking advice in ChIP-seq study design.
Fri, 12/13/2013 at 4:32 PM
Customer: I will do ChIP-seq with interested protein in two conditions, mitotic and interphase (total 6 samples with IgG and input) and same for MNase-seq (will confirm later sample no. ) in HEK293 cells. Do you have suggestions for ChIP experiment, such as platform preference?
Fri, 12/13/2013 at 6:11 PM
AccuraScience LB: I would suggest that you read this review article: http://www.ncbi.nlm.nih.gov/pubmed/23090257 when planning your ChIP-seq based studies. Box 1 of this review describes some of the general considerations for ChIP-seq experimental design.
We would recommend that you use Illumina's HiSeq platform. This is most cost-effective and this model of sequencers are easy to find if you would like to shop around for the best deal.
For your ChIP-seq experiments with the protein, 20 million reads should be good enough for any sample (IgG and input DNA included), thus 6 samples would fit in one lane (which produces 120-180 million reads). You have 6 samples + 12 control samples (are you sure you would want both IgG and input DNA controls?), which will occupy 3 lanes. Your MNase-seq experiments would need 40 million reads (rather than 20 million) per sample, so you can only fit 3 samples in a lane. One lane of experiment would cost you somewhere around $3,000 to do (I would suggest that you get quotes from a couple of sequencing labs and compare them), so you are looking at $10,000 for the protein ChIP-seq...
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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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