In this issue:



• Announcements
• 2024 Core Director Award Winners
• Cores Day Video Presentations Now Available
• Research Resource Identifier (RRID) Initiative Reminder
• ABRF Annual Meeting - March 23-26, 2025
• Core Facilities Spotlight
• OCRC Tumor BioTrust Collection
• Penn Genomic and Sequencing Core Facility (PGSC)
• Proteomics Core Facility

Announcements: 2024 Core Director Award Winners

We are delighted to announce that, following a review by a sub-group of our Cores Committee, Drs. Chris Petucci and Peter Cronholm have been selected as the winners of our 2024 Core Director Awards.

Dr. Chris Petucci has served as Director of the Penn Metabolomics Core Facility since its inception in 2018. Under his leadership, the core provides essential support in untargeted and targeted quantitative metabolomics. His team’s collaborative expertise supports a wide and active userbase, while also generating impactful data for research grants, publications, and new biomarker discoveries. Dr. Petucci has developed over ten custom targeted assays, while also advising on experimental design and data interpretation. Furthermore, Dr. Petucci currently serves as Core Director Meeting Chair, with the aim of creating an open dialogue to increase unity amount core directors while promoting core facility excellence.

Dr. Peter Cronholm has led the Mixed Methods Research Lab (MMRL) since co-leading its establishment in 2009, and has transformed it into a key resource for research support across Penn and beyond. As Director, Dr. Cronholm has standardized rigorous research procedures, implemented a sustainable cost model, and extended the core’s reach to a large and varied userbase. Known for his mentorship, Dr. Cronholm actively supports researchers at all levels, guiding many faculty from K-level to R01 grants and ensuring staff professional growth. Through his leadership, the MMRL has facilitated the creation of volumes of peer-reviewed publications, enriching the scientific community's knowledge base. 

We are honored to recognize the tremendous accomplishments of Drs. Petucci and Cronholm as Core Facility Directors and are grateful for their continued efforts to achieve excellence as part of our PSOM Biomedical Research Core Facility Community.

Announcements: Cores Day 2024 Video Presentations Now Available

Penn Cores Day video presentations are now available on demand as part of  the Core Facilities Mediasite Channel. The channel is designed to be a go-to resource for both core facility directors and potential customers. These videos are not just a snapshot in time, but can also serve as an enduring resource you may wish to share with interested users. Please contact April Weakley (aweakley@pennmedicine.upenn.edu) if you would like to provide updates or additional content. 

Announcements: Research Resource Identifier (RRID) Initiative Reminder

Please remember to encourage investigators to use your RRID when citing your core in publications.

RRID citations help showcase your work on the Core Facility Marketplace, and also allow for helpful indexing on PubMed and Google Scholar.

Several ideas to increase your RRID’s visibility can be found here: https://coremarketplace.org/blog/manual/rrid-use

If your core facility has not yet obtained an RRID, please visit the links below to learn more and feel free to contact April Weakley (aweakley@pennmedicine.upenn.edu) should you wish to obtain one. 

• https://www.med.upenn.edu/cores/core-facility-rrids.html
• https://coremarketplace.org/

Announcements: ABRF Annual Meeting - March 23-26, 2025

The Association of Biomolecular Resources Facilities (ABRF) Annual Meeting is an international program that provides timely updates on cutting-edge science and its execution in a shared resource/core facility setting. These meetings also offer informative and practical workshops as well as ample networking opportunities with academics, corporate, and technology partner colleagues. This year's meeting will be held from March 23-26 in Las Vegas, and ABRF members receive a discount when registering. Please click here for more information.

If you are not yet a member, we encourage you to visit the ABRF website , and to contact April Weakley (aweakley@pennmedicine.upenn.edu) if you would like to join the organization at no charge to you via PSOM’s institutional membership. 

Core Facilities Spotlight: OCRC Tumor BioTrust Collection - RRID:SCR_022387

The Ovarian Cancer Research Center Tumor BioTrust Collection collects fresh cancer tissue specimens, as well as plasma, serum, peripheral blood mononuclear cells (PBMC), blood and other biological samples from various cancer cases with a focus on gynecologic cancers. We also house formalin fixed paraffin embedded (FFPE) samples including tissue microarray (TMA) construction and immunohistochemistry. Samples collected through the Penn Legacy Tissue Program (PLTP) (e.g., rapid autopsy) are also available and a quote can be provided upon request.

We will also work with investigators to prospectively collect specific samples to support their research within Penn research community as well as in outside academic institutions. We will be working with biotech/bio-pharma companies if it is within the confines of a collaboration.



We are excited to announce that we have partnered with Pancreatic Cancer Research Center since 2022 to help launch and develop their new rapid autopsy program while we further develop and support our established program. Ultimately, we would like to have our Penn Legacy Tissue Program (PLTP) expanded to other disease/cancer sites at Penn and encourage them to engage with us without fully investing into establishing a formal program like ours. Please contact for more information.

Representative Publications:

CD137+ tumor infiltrating lymphocytes predicts ovarian cancer survival.

Elizabeth A Tubridy, Monika A Eiva, Fang Liu, Dalia K Omran, Stefan Gysler, Erica G Brown, Allison G Roy, Yuyan Zeng, Jinhee Oh, Quy Cao, Sarah B Gitto, Daniel J Powell Jr PMID: 38290413 DOI: 10.1016/j.ygyno.2024.01.029

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors.

Hippen, A.A., Omran, D.K., Weber, L.M. et al. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors. Genome Biol 24, 239 (2023). https://doi.org/10.1186/s13059-023-03077-7

Functional neuronal circuits promote disease progression in cancer.

Restaino AC, Walz A, Vermeer SJ, Barr J, Kovács A, Fettig RR, Vermeer DW, Reavis H, Williamson CS, Lucido CT, Eichwald T, Omran DK, Jung E, Schwartz LE, Bell M, Muirhead DM, Hooper JE, Spanos WC, Drapkin R, Talbot S, Vermeer PD.

Science Advances 2023 May 10;9(19):eade4443. doi: 10.1126/sciadv.ade4443.

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker.

Taylor MS, Connie W, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cheng WC, Heaps J, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Norden BL, Chait BT, Goggins M, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Jung E, Arora KS, Zukerberg LR, Yilmaz OH, Chi G, Matulonis UA, Song Y, Nieman L, Parikh AR, Strickland M, Corcoran RB, Mustelin T, Eng G, Yilmaz ÃH, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH.

BioRxiv 2023 Mar 17:2023.01.25.525462. doi: 10.1101/2023.01.25.525462. Preprint

Folate Receptor Beta as a Direct and Indirect Target for Antibody-Based Cancer Immunotherapy

Allison G. Roy, J. Michael Robinson, Prannda Sharma, Alba Rodriguez-Garcia, Mathilde A. Poussin, Cheryl Nickerson-Nutter, and Daniel J. Powell, Jr.

https://pubmed.ncbi.nlm.nih.gov/34070369

Intra-Tumoral Nerve-Tracing in a Novel Syngeneic Model of High-Grade Serous Ovarian Carcinoma.

Barr JL, Kruse A, Restaino AC, Tulina N, Stuckelberger S, Vermeer SJ, Williamson CS, Vermeer DW, Madeo M, Stamp J, Bell M, Morgan M, Yoon J-Y, Mitchell MA, Budina A, Omran DK, Schwartz LE, Drapkin R, Vermeer PD. Cells. 2021; 10(12):3491.

https://doi.org/10.3390/cells10123491

Systematic analysis of CD39, CD103, CD137, and PD-1 as biomarkers for naturally occurring tumor antigen-specific TILs.

Eiva MA, Omran DK, Chacon JA, Powell DJ Jr.

Eur J Immunol. 2021 Sep 10. doi: 10.1002/eji.202149329. Epub ahead of print.

https://pubmed.ncbi.nlm.nih.gov/34505280/

CAR-T cell-mediated depletion of immunosuppressive tumor-associated macrophages promotes endogenous antitumor immunity and augments adoptive immunotherapy.

Rodriguez-Garcia A, Lynn RC, Poussin M, Eiva MA, Shaw LC, O'Connor RS, Minutolo NG, Casado-Medrano V, Lopez G, Matsuyama T, Powell DJ Jr.

Nat Commun. 2021 Feb 9;12(1):877. doi: 10.1038/s41467-021-20893-2.

https://pubmed.ncbi.nlm.nih.gov/33563975/

Inhibition of relaxin autocrine signaling confers therapeutic vulnerability in ovarian cancer.

Burston HE, Kent OA, Communal L, Udaskin ML, Sun RX, Brown KR, Jung E, Francis KE, La Rose J, Lowitz JK, Drapkin R, Mes-Masson AM, Rottapel R.

J Clin Invest. 2021 Feb 9:142677. doi: 10.1172/JCI142677.

https://pubmed.ncbi.nlm.nih.gov/33561012/

Combining PARP with ATR inhibition overcomes PARP inhibitor and platinum resistance in ovarian cancer models.

Kim H, Xu H, George E, Hallberg D, Kumar S, Jagannathan V, Medvedev S, Kinose Y, Devins K, Verma P, Ly K, Wang Y, Greenberg RA, Schwartz L, Johnson N, Scharpf RB, Mills GB, Zhang R, Velculescu VE, Brown EJ, Simpkins F.

Nat Commun. 2020 Jul 24;11(1):3726. doi: 10.1038/s41467-020-17127-2.

https://pubmed.ncbi.nlm.nih.gov/32709856/

Core Facilities Spotlight: Penn Genomic and Sequencing Core Facility (PGSC) - RRID:SCR_02499

The Penn Genomics and Sequencing Core undertakes all phases of genomics and sequencing projects, from consultation and experimental design to data analysis.

Next Gen Sequencing (NGS)

• Illumina NovaSeq X Plus: 1.5B – 25B reads, being installed, less sequencing cost,***
• llumina NextSeq 2000: 100M – 1.8B reads
• Illumina MiSeq: 1M – 25M reads
• PacBio Revio: 30x HiFi long read human genome per SMRT Cell***
• Oxford Nanopore Minion: 2 – 25Gbp long read throughput per flow cell***

NGS Library Construction

• DNA/RNA isolation from blood, saliva, tissue (including FFPE) and cells
• DNA-Seq: Whole exome/genome and targeted panels Bulk RNA-Seq and miRNA-Seq
• 10X Genomics Single Cell Gene Expression (Multiome coming soon)
• Long read libraries for ONT and PacBio
• Library QC Service: qPCR, Qubit, Bioanalyzer and TapeStation
• Covaris DNA shearing on M220 and LE220 sonicators
• Blue Pippin size selection

Sanger Sequencing & Other Platforms

• Sanger Sequencing: 24 – 36 hour turnaround
• Human cell line authentication***
• Fragment sizing: Microsatellite, VNTR, SNaPshot
• qPCR, dPCR, and aCGH for gene expression, mutation validation and CNV detection

Informatics & Support

• Free consultation for planning, experimental design, grants and publications Custom sequencing and profiling assay design
• Full bioinformatics support, independent of data origin

Contact Us

Next Generation Sequencing

ngsc@pennmedicine.upenn.edu

Sanger Sequencing and Fragment Analysis

dnaseq@pennmedicine.upenn.edu

Tapan Ganguly, PhD; Director

215-573-7238

gangulyt@pennmedicine.upenn.edu

Erik Toorens; Technical Director

toorens@pennmedicine.upenn.edu

John Tobias, PhD; Bioinformatics

jtobias@pennmedicine.upenn.edu

Core Facilities Spotlight: CHOP-Penn Proteomics Core Facility - RRID_SCR:023099

Exploring the complex roles of proteins in disease onset, diagnosis, and treatment has been challenging due to the biological complexity of samples and technological limitations. To address some of these challenges, the CHOP-PENN Proteomics Core (RRID:SCR_023099) is excited to announce the addition of two advanced instruments for quantitative proteomics: the Olink Signature Q100 and the SEER Proteograph XT platform. 

Olink Signature Q100 

The Olink Signature Q100 is designed for multiplexed, targeted protein assays using Proximity Extension Assay (PEA) technology. This dual recognition DNA-coupled methodology ensures exceptional specificity and high-throughput biomarker analysis. 

Key features include: 

• Olink 96 panels for disease-specific biomarkers and biological processes 
• Olink 48 panels for cytokine signaling and inflammatory processes, with extensive validation 
• Access to all Olink Target protein panels for specific disease areas or biological processes 

SEER Proteograph XT Platform 

The SEER Proteograph XT platform enables deep, unbiased, discovery-based proteomics analysis of biofluids such as plasma, serum, and CSF. This platform offers reproducible, quantitative detection of thousands of proteins per sample, regardless of species. It leverages automated workflows and engineered nanoparticle technology to enhance protein detection sensitivity, making it a game-changer for LC-MS/MS analysis. 

The Proteograph XT platform creates opportunities for unbiased proteomics research in: 

• Biomarker discovery and diagnostic development 
• Precision and personalized medicine 
• Disease mechanism research 
• Drug target discovery 

For more information or to discuss how these technologies can support your research, please contact us at proteomics@chop.edu. 

Lynn Spruce

Technical Director

CHOP-PENN Proteomics Core Facility www.research.chop.edu/chop-penn-proteomics-core

806 ARC

3616 Civic Center Blvd.

Philadelphia, PA 19104

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