Guide to the Datasets



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.


Guide to the Data Sets


2022

Cobo I, Cheng A, Murillo-Saich J, Coras R, Torres A, Abe Y, Lana AJ, Schlachetzki J, Liu-Bryan R, Terkeltaub R, Sanchez-Lopez E, Glass CK. Monosodium urate crystals regulate a unique JNK-dependent macrophage metabolic and inflammatory response Cell Reports, 2022. https://doi.org/10.1016/j.celrep.2022.110489


2021

Hoeksema MA, Shen Z, Holtman IR, Zheng A, Spann NJ, Cobo I, Gymrek M, Glass CK. Mechanisms underlying divergent responses of genetically distinct macrophages to IL-4. Sci Adv. 2021 Jun 16;7(25):eabf9808. doi: 10.1126/sciadv.abf9808. PMID: 34134993.


2020

Seidman JS, Troutman TD, Sakai M, Gola A, Spann NJ, Bennett H, Bruni CM, Ouyang Z, Li RZ, Sun X, Vu BT, Pasillas MP, Ego KM, Gosselin D, Link VM, Chong L, Evans RM, Thompson BM, McDonald JG, Hosseini M, Witztum JL, Germain RN, Glass CK. Niche-Specific Reprogramming of Epigenetic Landscapes Drives Myeloid Cell Diversity in Nonalcoholic Steatohepatitis. Immunity. 2020 Apr 28;S1074-7613(20)30159-X. doi: 10.1016/j.immuni.2020.04.001. PMID: 32362324.


Sajti E, Link VM, Ouyang Z, Spann NJ, Westin E, Romanoski CE, Fonseca GJ, Prince LS, Glass CK. Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung. Nat Immunol. 2020 Feb;21(2):221-231. doi: 10.1038/s41590-019-0582-z. Epub 2020 Jan 20. PMID: 31959980.



2019

Nott A*, Holtman IR*, Coufal NG*, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiaoi J, Wu Y, Keulen Z, Pasillas MP, O’Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. Science. 2019 Nov 14. pii: eaay0793. doi: 10.1126/science.aay0793.



Sakai M, Troutman TD, Seidman JS, Ouyang Z, Spann NJ, Abe Y, Ego KM, Bruni CM, Deng Z, Schlachetzki JCM, Nott A, Bennett H, Chang J, Vu BT, Pasillas MP, Link VM, Texari L, Heinz S, Thompson BM, McDonald JG, Geissmann F, Glass CK. Liver-Derived Signals Sequentially Reprogram Myeloid Enhancers to Initiate and Maintain Kupffer Cell Identity. Immunity. 2019 Oct 3. DOI: https://doi.org/10.1016/j.immuni.2019.09.002.


Fonseca GJ, Tao J, Westin EM, Duttke SH, Spann NJ, Strid T, Shen Z, Stender JD, Sakai M, Link VM, Benner C, Glass CK. Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages. Nat Commun. 2019 Jan 24;10(1):414. doi: 10.1038/s41467-018-08236-0.



2018

Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. Cell June 17, 2018. https://doi.org/10.1016/j.cell.2018.04.018



2017

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.


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.


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.



2016

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.


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.


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.



2014

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.


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.



2013

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.


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).


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.


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.



2012

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.



2011

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.



2010

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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University of California, San Diego School of Medicine
University of California, San Diego