Guide to the Data Sets


The publications listed below include RNA-Seq, ChIP-Seq and other genome-wide data sets that have been deposited with GEO. Clicking the title takes you to the PubMed page for the article and clicking the GEO-Link button takes you to the corresponding GEO accession page.


SELECTED PUBLICATIONS

1. Hogan NT, Whalen MB, Stolze LK, Hadeli NK, Lam MT, Springstead JR, Glass CK, Romanoski CE. Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells. Elife. 2017 Jun 6;6. pii: e22536. doi: 10.7554/eLife.22536.


2. Gosselin D, Skola D, Coufal NG, Holtman IR, Schlachetzki JCM, Sajti E, Jaeger BN, O'Connor C, Fitzpatrick C, Pasillas MP, Pena M, Adair A, Gonda DG, Levy ML, Ransohoff RM, Gage FH, Glass CK. An environment-dependent transcriptional network specifies human microglia identity. Science. 2017 May 25. pii: eaal3222. doi: 10.1126/science.aal3222. [Epub ahead of print] PubMed PMID: 28546318.


2. Stender JD, Nwachukwu JC, Kastrati I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Rangarajan ES, Carlson KE, Katzenellenbogen JA, Yao X, Grant BJ, Leong HS, Lin C, Frasor J, Nettles KW, Glass CK. Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells. Mol Cell. 2017 Mar 16;65(6):1122-1135.e5. doi: 10.1016/j.molcel.2017.02.008.PMID: 27814941.


3. Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK. SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. Cell Metab. 2016 Dec 21.


4. Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK. Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. Elife. 2016 Jul 27;5. pii: e13024. doi: 10.7554/eLife.13024.


5. Allison KA, Sajti E, Collier JG, Gosselin D, Troutman TD, Stone EL, Hedrick SM, Glass CK. Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. Elife. 2016 Jul 4;5. pii: e10134. doi: 10.7554/eLife.10134.


6. Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Gerner H, Geissmann F, Glass CK. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 2014 159(6):1327-1340.


7. Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK. Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. Nat Neurosci. 2014 PMID: 24584051.


8. Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. Effect of natural genetic variation on enhancer selection and function. Nature. 2013 503(7477):487-92 PMID: 24121437 PMCID: PMC3994126.


9. Li P, Spann NJ, Lu M, Oh D, Yamamoto H, Auwerx J, Bandyopadhyay G, Patsouris D, Dennis EA, Watkins SM, Glass CK*, Olefsky JM*. NCoR KO reprograms macrophages lipid metabolism increasing ω3 fatty acids synthesis and insulin sensitivity. Cell. 2013 155:200-14. PMID: 24074869 (*co-corresponding authors).


10. Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. Mol. Cell. 2013 53:310-325. PMID: 23932714.


11. Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK. Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature. 2013 498:511-5. PMID: 23728303 PMCID: PMC3839578.


12.Stender JD, Pascual G, Liu W, Kaikkonen MU, Do K, Spann NJ, Boutros M, Perrimon N, Rosenfeld MG, Glass CK. Control of Proinflammatory Gene Programs by Regulated Trimethylation and Demethylation of Histone H4K20. Mol Cell. 2012 48(1):28-38 Aug 21. PMID: 22921934 PMCID: PMC3472359.


13. Escoubet-Lozach L, Benner C, Kaikkonen M, Lozach J, Heinz S, Spann NJ, Crotti A, Stender JD, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik C, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass, C.K. Mechanisms establishing TLR4-Responsive activation states of inflammatory response genes. PLoS Genetics. 2011 Dec;7(12):e1002401. PMID: 22174696.


14. Heinz S, Benner C, Spann NJ, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass, C.K. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 2010 38:576-89. PMID: 20543837.



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