Computational protocol: Interconversion between active and inactive TATA-binding protein transcription complexes in the mouse genome

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Protocol publication

[…] Chromatin immunoprecipitation (ChIP) and ChIP-seq experiments were performed according to standard protocols as previously described (,). Briefly, ChIP-seq was performed using an Illumina GAIIx sequencer and the raw data analysed by the Illumina Eland pipeline V1.6. Peak detection was performed using the MACS software (http://liulab.dfci.harvard.edu/MACS/) () under settings where the GFP ChIP was used as a negative control. Peaks were then annotated using GPAT [(), http://bips.u-strasbg.fr/GPAT/Gpat_home.html] using a window of ±10 kb with respect to the coordinates of the beginning and end of RefSeq transcripts. Global clustering analysis and quantitative comparisons were performed using seqMINER [() (http://bips.u-strasbg.fr/seqminer/]. Further details are provided in the Supplementary Data. ChIP was performed with the following antibodies; TBP (Abcam, AB28175), Pol II, MED6, XPB, TFIIB (Santa Cruz SC-9001, SC-9434, C18-CS225, respectively), H3K4me3 (Upstate 07-473). The TAF1 antibody was a kind gift from Dr. L. Tora. […]

Pipeline specifications

Software tools ELAND, seqMINER
Application ChIP-seq analysis
Organisms Mus musculus, Homo sapiens