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University of Pennsylvania Perelman School of Medicine Cell and Developmental Biology Microscopy Core Facility

University of Pennsylvania

Contact Info:

Andrea Stout

https://www.med.upenn.edu/cdbmicroscopycore/

Grants and Identifiers:

RRID: RRID:SCR_022373

Instrumentation:

Services Provided:

Relevant Publications:

1.) Rood JE, Yoon SK, Heard MK, Carro SD, Hedgepeth EJ, O'Mara ME, Hogan MJ, Le N, Muramatsu H, Lam K, Schreiner P, Kasden C, Stedman HH, Langlois RA, Heyes J, Pardi N, Eisenlohr LC (2026 Jan 16). Optimal murine CD4(+) T cell priming by mRNA-lipid nanoparticle vaccines requires endogenous antigen processing. Nature communications, 17(1), 1327. . PMCID: 12873236.


2.) Li D, Loneker AE, Safraou Y, Ford J, Mihelc E, Sakane S, Kisseleva T, Levental KR, Levental I, Sack I, Janmey PA, Wells RG (2026 Jan 13). Cholesterol-containing lipid crystals can directly stiffen the rat steatotic liver before fibrosis. Proceedings of the National Academy of Sciences of the United States of America, 123(2), e2518060123. . PMCID: 12799114.


3.) Boudreault S, Rivera-Lopez Y, Ferretti MB, Tracey MA, Bonner J, Jacobs BL, Lynch KW (2026 Jan 13). Nonsense-mediated decay controls a negative feedback loop in innate immune sensing. Proceedings of the National Academy of Sciences of the United States of America, 123(2), e2517478123. . PMCID: 12799163.


4.) Pruzinsky E, Batmanov K, Medeiros DM, Sulon SM, Sullivan BP, Sakamoto T, Leone TC, Khurana TS, Kelly DP (2025 Nov 24). A role for the transcriptional coregulator RIP140 in the control of muscle endurance fitness. JCI insight, 10(22), . . PMCID: 12643488.


5.) Karakasheva TA, Martinez CM, Zhou Y, Qui J, Chen XE, Soto GE, Nettleford SK, Hix OT, Roach DM, Laguerta AM, Thadi A, Edwards RM, Aleynick D, Weinbrom S, Borodyanskaya E, Pickering OH, Fulton M, Chen CH, Peterson IV, Hagen EB, Yannuzzi IP, Haider Z, Cramer Z, Conrad MA, Li N, Bewtra M, Uzun Y, Tan K, Kelsen JR, Minn AJ, Lengner CJ, Hamilton KE (2025 Oct 20). An Epigenetic Basis for Sustained Inflammatory Epithelial Progenitor Cell States in Crohn's Disease. Cellular and molecular gastroenterology and hepatology, 20(3), 101665. . PMCID: 12721313.


6.) Waldman AJ, Pham K, Titus KR, Nikish A, Liu C, Ryu HS, Muppidi SS, Chandradoss KR, Xu P, Patel R, Boya R, Phillips-Cremins JE (2025 Oct 1). Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons. bioRxiv : the preprint server for biology, (), . . PMCID: 12621786.


7.) Panthi A, Ferretti MB, Howard O, Pokharel SM, McCracken R, Boudreault S, Quesnel-Vallieres M, Li Q, Cherry S, Lynch KW (2025 Sep 23). Alternatively spliced isoforms of IRF7 differentially regulate interferon expression to tune response to viral infection. Cell reports, 44(9), 116166. . PMCID: 12401477.


8.) Mukherjee A, Kapoor M, Shankta K, Fallacaro S, Carter RD, Hayward-Lara G, Ratchasanmuang P, Haloush YI, Mir M (2025 Sep 16). A single cluster of RNA Polymerase II molecules is stably associated with active genes. bioRxiv : the preprint server for biology, (), . . PMCID: 11844394.


9.) Voos KM, Tzeng J, Patel P, Rubinsky S, Choi HE, Pharr T, Sookram S, Baur JA, Soderblom EJ, Lorenzo DN (2025 Aug 25). Ankyrin-B modulates mitochondrial fission in skeletal muscle and is required for optimal endurance exercise capacity. Nature communications, 16(1), 7671. . PMCID: 12379235.


10.) Vázquez Marrero VR, Doerner J, Wodzanowski KA, Zhang J, Lu A, Boyer FD, Vargas I, Hossain S, Kammann KB, Dresler MV, Shin S (2025 Jul 9). Dendritic cells activate pyroptosis and effector-triggered apoptosis to restrict Legionella infection. mBio, 16(7), e0125725. . PMCID: 12239575.


11.) Wiest A, Maurer JJ, Beier KT, Weber F, Chung S (2025 Jul 2). Role of Hypothalamic CRH Neurons in Regulating the Impact of Stress on Memory and Sleep The Journal of Neuroscience, 45(27), e2146242025. . PMCID: 12225598.


12.) Dooling LJ, Anlaş AA, Tobin MP, Ontko NM, Marchena T, Wang M, Andrechak JC, Discher DE (2025 Jul 1). Clustered macrophages cooperate to eliminate tumors via coordinated intrudopodia Proceedings of the National Academy of Sciences of the United States of America, 122(27), e2425452122. . PMCID: 12260397.


13.) Yang X, Zanfardino A, Schiaffini R, Ishibashi J, Daniel B, Haemmerle MW, Rapini N, Piscopo A, Miraglia Del Giudice E, Digilio MC, Iorio R, Mucciolo M, Cianfarani S, Iafusco D, Barbetti F, Stoffers DA (2025 Jun 9). Neonatal diabetes-associated missense PDX1 variant disrupts chromatin association and protein-protein interaction. JCI insight, 10(11), . . PMCID: 12220937.


14.) Beyer JN, Serebrenik YV, Toy K, Najar MA, Feierman E, Raniszewski NR, Korb E, Shalem O, Burslem GM (2025 May). Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins. Science (New York, N.Y.), 388(6746), eadr5499. . PMCID: 12811073.


15.) Mukhi D, Kolligundla LP, Doke T, Silva MA, Liu H, Palmer M, Susztak K (2025 Apr 22). The actin and microtubule network regulator WHAMM is identified as a key kidney disease risk gene. Cell reports, 44(4), 115462. . PMCID: 12181807.


16.) Sande CM, Chen S, Mitchell DV, Lin P, Abraham DM, Cheng JM, Gebhard T, Deolikar RJ, Freeman C, Zhou M, Kumar S, Bowman M, Bowman RL, Zheng S, Munkhbileg B, Chen Q, Stanley NL, Guo K, Lapite A, Hausler R, Taylor DM, Corines J, Morrissette JJ, Lieberman DB, Yang G, Shestova O, Gill S, Zheng J, Smith-Simmer K, Banaszak LG, Shoger KN, Reinig EF, Peterson M, Nicholas P, Walne AJ, Dokal I, Rosenheck JP, Oetjen KA, Link DC, Gelman AE, Reilly CR, Dutta R, Lindsley RC, Brundige KJ, Agarwal S, Bertuch AA, (2025 Apr 15). ATM-dependent DNA damage response constrains cell growth and drives clonal hematopoiesis in telomere biology disorders. The Journal of clinical investigation, 135(8), . . PMCID: 11996883.


17.) Uchida K, Scarborough EA, Prosser BL (2025 Feb 11). Dual Translational Control in Cardiomyocytes by Heterogeneous mTORC1 and Hypertrophic ERK Activation. bioRxiv : the preprint server for biology, (), . . PMCID: 11844361.


18.) Niethamer TK, Planer JD, Morley MP, Babu A, Zhao G, Basil MC, Cantu E, Frank DB, Diamond JM, Nottingham AN, Li S, Sharma A, Hallquist H, Levin LI, Zhou S, Vaughan AE, Morrisey EE (2025 Feb 6). Longitudinal single-cell profiles of lung regeneration after viral infection reveal persistent injury-associated cell states. Cell stem cell, 32(2), 302-321.e6. . PMCID: 11805657.


19.) Nelson KA, Lenhart KF, Anllo L, DiNardo S (2025 Jan 3). The Drosophila hematopoietic niche assembles through collective cell migration controlled by neighbor tissues and Slit-Robo signaling eLife, 13(), RP100455. . PMCID: 11698496.


20.) Kollmar J, Xu J, Gonzalves D, Baur JA, Li LZ, Tchou J, Xu HN (2024 Dec 24). Differential Mitochondrial Redox Responses to the Inhibition of NAD(+) Salvage Pathway of Triple Negative Breast Cancer Cells. Cancers, 17(1), . . PMCID: 11718843.


21.) Swingle KL, Hamilton AG, Safford HC, Geisler HC, Thatte AS, Palanki R, Murray AM, Han EL, Mukalel AJ, Han X, Joseph RA, Ghalsasi AA, Alameh MG, Weissman D, Mitchell MJ (2024 Dec 11). Placenta-tropic VEGF mRNA lipid nanoparticles ameliorate murine pre-eclampsia Nature, 637(8045), 412-421. . PMCID: 12205896.


22.) Zhang D, Cleveland AH, Krimitza E, Han K, Yi C, Stout AL, Zou W, Dorsey JF, Gong Y, Fan Y (2024 Apr). Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy. Nature protocols, 19(4), 1053-1082. . PMCID: 12276897.


23.) Shoenhard H, Granato M (2023 Feb 14). Multivariate analysis of variegated expression in Neurons: A strategy for unbiased localization of gene function to candidate brain regions in larval zebrafish PLOS ONE, 18(2), e0281609. . PMCID: 9928119.


Description:

Core provides personalized assistance on all aspects of imaging, from tips on sample preparation to training on one of our microscopes to assistance with image data analysis. Facility houses confocal microscopes, a Zeiss Z.1 Lightsheet system, three widefield light microscopes, and several computers dedicated to image processing and analysis. Offers scanning electron microscope sample preparation and imaging.