Computational protocol: 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism

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Protocol publication

[…] Putative dioxin response elements (pDREs) with matrix similarity scores (MSS) ≥ 0.856 were previously identified. ChIP-Seq was previously performed on liver samples from male C57BL/6 mice 2 h after a single bolus oral gavage of 30 µg/kg TCDD, . Briefly, cross-linked DNA was immunoprecipitated with either rabbit IgG or anti-AhR (H-211, sc-5579; Santa Cruz, CA). Libraries were prepared using the MicroPlex kit (Diagenode), pooled, and sequenced at a depth of a ~30 M on an Illumina HiSeq 2500 at the MSU RTSF Genomics Core. Reads were mapped to the mouse reference genome (GRCm38 release 81) using Bowtie 2.0.0 and alignments converted to SAM format using SAMTools v0.1.2. Normalization and peak calling was performed using CisGenome, by comparing IgG control and AhR enriched samples (n = 5) using a bin size (−b) of 25 and boundary refinement resolution (−bw) of 1 with default parameters. […]

Pipeline specifications

Software tools Bowtie, SAMtools, CisGenome
Application ChIP-seq analysis
Organisms Mus musculus, Homo sapiens
Chemicals Bile Acids and Salts, Cholesterol, Taurolithocholic Acid