Chip-chip from E. coli MG1655 cells with different methods to detect SeqA and σ32 binding and causes of high background

ABSTRACT: Reinvestigation of the chromatin immunoprecipitation procedure led us to discover four causes of high background: non-unique sequences, incomplete reversion of crosslinks, washing with spin-columns and insufficient RNase treatment. We used a publishd method giving a high background signal and a modified chromatin immunoprecipitation method which could greatly reduce the false positive rate and apply it to analyze genome wide binding of SeqA and σ32 binding in E. coli. RNA polymerase binding in wt E. coli MG1655 with old method (two biological relpicates); comparison of SeqA-binding to wt with old and modified method (two biological replicates each); comparison of SeqA-binding with old and modified method to E. coli ΔseqA (one array each); comparison of crosslinked/reversed to non crosslinked E. coli chrom. DNA; σ32 binding at 30°C and 43°C (two biological replicates each); σ32 binding at 30°C and 43°C with shortened RNase digestion during ChIP (one array each).

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Torsten Waldminghaus 

PROVIDER: E-GEOD-19053 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress