Cells were fixed in 1% formaldehyde at room temperature for 20 min, quenched with glycine, and lysed. Chromatin was pelleted and solublized by sonication. Crosslinked chromatin was then immunoprecipitated.
Label
Cy5
Label protocol
ChIP DNA was first denatured and 2-cycle-amplified amplified using primer A (5'-GTTTCCCAGTCACGATCNNNNNNNNN); the resulting DNA was then subjected to a 35-round amplification using primer B (5'-TCCCAGTCACGATC).
Hybridization protocol
Labeled DNA was hybridized and scanned using proprietary methods (NimbleGen).
Scan protocol
Labeled DNA was hybridized and scanned using proprietary methods (NimbleGen).
Description
ChIP DNA
Data processing
Linearly scaled so that intensity values in Sigma70_ChIP_control_A_cy3, Sigma70_ChIP_A_cy5, Sigma70_ChIP_control_B_cy3, Sigma70_ChIP_B_cy5, Beta_ChIP_control_A_cy3, Beta_ChIP_A_cy5, Beta_ChIP_control_B_cy3, Beta_ChIP_B_cy5 are comparable
