Missing Enrichments

[andibody]

Hi,

I have been performing ChIP-Seq for our institute the last half a year with mostly good results. Nevertheless, some samples behave 'strange'.
The scientists performing the ChIP check enrichment via qPCR before the samples are accepted for sequencing. In some cases we are not
able to see these enrichments after sequencing although the results look otherwise
OK (distribution over the genome, enrichment of adapter ligated fragments etc.).
Has anybody experienced similar troubles? Or uses any additional control before starting with sample prep?
Could I be distorting my ratios during sample prep PCR ?

Thanks for any answers/comments

[Chipper]

We have had some cases like this, but I do not yet know what is causing it. Have you compared the bad runs to the good ones in term of sonication level and number of cycles needed to get the qPCR signal?

[andibody]

Since we use a Covaris sonicator scientists report highly reproducible shearing, from the images of input sample on agarose gels, the size distribution isn't different in good and bad runs. The number of cycles needed for detection of differences in input and ip varies strongly depending on the selected site for testing and ranges between 10 and 30 cycles.