Computational protocol: Control of Smc Coiled Coil Architecture by the ATPase Heads Facilitates Targeting to Chromosomal ParB/parS and Release onto Flanking DNA

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Protocol publication

[…] ChIP samples were prepared as described above with the exception that several immunoprecipitate (IP) samples were loaded onto the same PCR purification column to obtain sufficient DNA material. DNA (1–5 ng) was analyzed by Illumina sequencing at the Max Planck Genome Centre in Cologne. Briefly, DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–280 bp with a main peak of ∼250 bp. DNA libraries were prepared using the Ovation Ultralow Library System (NuGEN) kit (version V1) including 15 cycles of PCR amplification. Five to ten million sequence reads were obtained on a HiSeq2500 (Illumina) with 100-bp read length. The obtained reads were mapped to the genome with Bowtie (http://GalaxyProject.org) using default settings and randomly assigning sequencing reads from repetitive DNA elements to a single location. Subsequent data analysis was performed using Seqmonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and Microsoft Excel. […]

Pipeline specifications

Software tools Bowtie, SeqMonk
Application ChIP-seq analysis
Organisms Bacillus subtilis
Chemicals Adenosine Triphosphate