Description of an optimized ChIP-seq analysis pipeline dedicated to genome wide identification of E4F1 binding sites in primary and transformed MEFs

Genomics Data - Tập 5 - Trang 368-370 - 2015
Thibault Houlès1, Geneviève Rodier1, Laurent Le Cam1, Claude Sardet1, Olivier Kirsh1
1Inserm U1194, Université Montpellier, Institut Régional du Cancer de Montpellier (ICM), 208 rue des Apothicaires, 34298 Montpellier, France

Tài liệu tham khảo

Le Cam, 2004, The E4F protein is required for mitotic progression during embryonic cell cycles, Mol. Cell. Biol., 24, 6467, 10.1128/MCB.24.14.6467-6475.2004 Le Cam, 2006, E4F1 is an atypical ubiquitin ligase that modulates p53 effector functions independently of degradation, Cell, 127, 775, 10.1016/j.cell.2006.09.031 Fajas, 2000, pRB binds to and modulates the transrepressing activity of the E1A-regulated transcription factor p120E4F, Proc. Natl. Acad. Sci. U. S. A., 97, 7738, 10.1073/pnas.130198397 Hatchi, 2011, E4F1 deficiency results in oxidative stress-mediated cell death of leukemic cells, J. Exp. Med., 208, 1403, 10.1084/jem.20101995 Ji, 2008, An integrated software system for analyzing ChIP-chip and ChIP-seq data, Nat. Biotechnol., 26, 1293, 10.1038/nbt.1505 Lacroix, 2010, Transcription factor E4F1 is essential for epidermal stem cell maintenance and skin homeostasis, Proc. Natl. Acad. Sci. U. S. A., 107, 21076, 10.1073/pnas.1010167107 Micsinai, 2012, Picking ChIP-seq peak detectors for analyzing chromatin modification experiments, Nucleic Acids Res., 40, e70, 10.1093/nar/gks048 Raychaudhuri, 1987, Identification of an E1A-inducible cellular factor that interacts with regulatory sequences within the adenovirus E4 promoter, EMBO J., 6, 4073, 10.1002/j.1460-2075.1987.tb02753.x R Development Core Team Rodier, 2015, The transcription factor E4F1 coordinates CHK1-dependent checkpoint and mitochondrial functions, Cell Rep., 11, 220, 10.1016/j.celrep.2015.03.024 Zhang, 2008, Model-based analysis of ChIP-Seq (MACS), Genome Biol., 9, R137, 10.1186/gb-2008-9-9-r137