Computational protocol: FOXA1 potentiates lineage-specific enhancer activation through modulating TET1 expression and function

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Protocol publication

[…] Chromatin immunoprecipitation (ChIP) experiments were carried out as previously described (). All primers (listed in Supplementary Data) were designed using Primer 3 (http://frodo.wi.mit.edu/primer3/), synthesized by Integrated DNA Technologies and used for SYBR Green based real-time PCR. ChIP-quantitative PCR enrichment of target loci was normalized to input DNA and reported as Enrichment over input ±SEM. ChIP DNA was prepared into libraries according to standard protocols using Bioo Scientific's DNA Sample Kit (cat. no. 514101). Libraries were sequenced using Illumina Hi-Seq platforms. Sequence reads were aligned to the Human Reference Genome (assembly hg19) using Burrows–Wheeler alignment tool (bwa) version 0.6.1. New high-throughput data generated in this study have been deposited in GEO database under accession number GSE73363. […]

Pipeline specifications

Software tools Primer3, BWA
Application qPCR
Chemicals 5-Methylcytosine