Computational protocol: Differential gene expression along the animal-vegetal axis in the ascidian embryo is maintained by a dual functional protein Foxd

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Protocol publication

[…] We used a DNA construct encoding GFP-tagged Foxd under the control of the Foxd promoter []. Embryos were fixed at the 32-cell stage. The embryos were subjected to ChIP analysis using anti-GFP antibodies, and the immunoprecipitated DNA was amplified by ligation-mediated PCR []. Whole cell extract DNA was used as a control. Then, high-throughput DNA sequencing was performed with the Ion PGM instrument (SRA accession number: DRA005285). To identify peak regions, we used two different programs called Homer [] with options “-style factor -F 4 -P 0.01 -L 4 -localSize 3000” and MACS2 [] with an option “--nomodel -q 0.001". […]

Pipeline specifications

Software tools HOMER, MACS
Application ChIP-seq analysis
Organisms Ciona intestinalis, Caenorhabditis elegans