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Pipeline publication

[…] he other antibodies. Third, those IgG-subtracted percent-of-input values were reported as fractions of the values obtained with the wild-type CER polyclone., ChIP-seq experiments were performed on 50 million primary myoblasts in growth phase. Chromatin was fragmented to an average size of 200 bp and immunoprecipitated using rabbit anti-Six1 or a control rabbit IgG (Jackson). An input chromatin sample (prior to immunoprecipitation enrichment) was also prepared. After purification, sequencing libraries were prepared by the McGill University and Génome Québec Innovation Centre, and sequenced at 1 sample per lane on HiSeq2000. Sequencing reads were aligned to the mm9 mouse genome assembly using Bowtie in –n mode , allowing 0 mismatches in the first 36 nucleotides of each read, and removing reads that align at more than one location in the genome. Picard was used to filter out replicated reads (http://picard.sourceforge.net/). SeqMonk (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) was used to extend reads to a length of 200 bp, to normalize read counts to the total number of retained reads in each sample, and to calculate normalized read densities for each sample in contiguous, non-overlapping bins of 25 base pairs. The read density in the input sample was finally subtracted from the immunoprecipitation samples. These read densities are given as wiggle format files as . A full description of the ChIP-seq results will be published elsewhere (Y.L. and A.B., in preparation)., Full-length CER DNA probes were prepared by PCR amplification from wild-type or mutant plasmids, restriction digestion and fill-in with Klenow enzyme (Promega) in the presence of Cy5-label […]

Pipeline specifications

Software tools Bowtie, Picard, SeqMonk
Organisms Mus musculus