ChIP-seq for Histone Marks and TFs

ChIPs were performed from 5–10×10⁶ cross-linked cells and sequencing libraries were prepared as previously described^{52 (link)}. The following antibodies were used for ChIP: rabbit anti-H3K4me1 (Abcam #8895), rabbit anti-H3K27ac (Abcam #4729), rabbit anti-c-Fos (Santa Cruz #sc-52), rabbit anti-FOSL1/Fra-1 (Santa Cruz #sc-605). ChIP-seq libraries were sequenced on the HiSeq 2000 or 2500 platform at the Case Western Reserve University Genomics Core Facility.
Analysis was performed as previously described^{8 (link)}.

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Morrow J.J., Bayles I., Funnell A.P., Miller T.E., Saiakhova A., Lizardo M.M., Bartels C.F., Kapteijn M.Y., Hung S., Mendoza A., Dhillon G., Chee D.R., Myers J.T., Allen F., Gambarotti M., Righi A., DiFeo A., Rubin B.P., Huang A.Y., Meltzer P.S., Helman L.J., Picci P., Versteeg H., Stamatoyannopolus J., Khanna C, & Scacheri P.C. (2018). Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. Nature medicine, 24(2), 176-185.

Publication 2017

rabbit anti-H3K4me1 rabbit anti-H3K27ac rabbit anti-c-Fos rabbit anti-FOSL1/Fra-1

Antibodies Cells Chip Chip seq Fra 1 Rabbit

Corresponding Organization :

Other organizations : Case Western Reserve University, Altius Institute for Biomedical Sciences, National Cancer Institute, National Institutes of Health, Center for Cancer Research, Leiden University Medical Center, University of Washington, Istituto Ortopedico Rizzoli, Cleveland Clinic

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Variable analysis

independent variables

Amount of cross-linked cells (5–10×10^6)

dependent variables

ChIP-seq library sequencing

control variables

Antibodies used for ChIP: rabbit anti-H3K4me1, rabbit anti-H3K27ac, rabbit anti-c-Fos, rabbit anti-FOSL1/Fra-1

controls

Positive control: Not explicitly mentioned.
Negative control: Not explicitly mentioned.

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