ChIP Assay for Histone Modifications

Chromatin immunoprecipitation (ChIP) was done as described in Lindeman et al. [49 (link)]. Antibodies, H3K4me3 (cat #. C15410003), H3K27me3 (cat # C15410069) and H3-pan (cat# C15310135) were purchased from Diagenode, Belgium. ChIP-primers for cebpa locus were designed in Primer3 v4.0.0 [50 (link), 51 (link)] and purchased from ThermoFisher Scientific (Additional file 1: Table S1). The precipitated DNA was quantified with qPCR (SYBR green, Roche) using 2.5 µL ChIP DNA as input template. Both ChIP and the qPCR experiments were performed in duplicates.

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den Broeder M.J., Ballangby J., Kamminga L.M., Aleström P., Legler J., Lindeman L.C, & Kamstra J.H. (2020). Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish. Epigenetics & Chromatin, 13, 5.

Publication 2020

H3K27me3 H3-pan SYBR green

Antibodies Cebpa Chromatin immunoprecipitation H3k4me3 Primers Sybr green

Corresponding Organization :

Other organizations : Utrecht University, Norwegian University of Life Sciences, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center

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Variable analysis

independent variables

Antibody (H3K4me3, H3K27me3, H3-pan)

dependent variables

Enrichment of DNA fragments at the cebpa locus

control variables

ChIP protocol as described in Lindeman et al. [49]
Primer design using Primer3 v4.0.0 [50, 51]

controls

Positive control: ChIP with H3-pan antibody (pan-histone H3)
Negative control: Not explicitly mentioned

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