Pennsylvania State University

Contact Info:

Cheryl Keller

412 Chandlee Laboratory

University Park, PA 16802

https://www.huck.psu.edu/core-facilities/genomics-core-facility

Grants and Identifiers:

RRID: RRID:SCR_023645

Instrumentation:

Services Provided:

10x Genomics

DNA Analysis

Full Genome CDNA Screening

Genomics

Genotyping

Metagenomics Analysis

Metatranscriptomics

Microbiome

Real-time qPCR

RNA analysis

RNAseq

Sequencing - Capillary Sequencing

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Single-cell Sequencing

Whole Exome Sequencing

Whole Genome Sequencing

Relevant Publications:

1.) Sieg J, Zeng H, Pálová H, Smeds L, Mohanty S, Lahnsteiner A, Chiaromonte F, Makova KD (2025 Nov 4). Comparative analysis of single-stranded and non-canonical DNA formation in human and other ape cells with telomere-to-telomere genomes bioRxiv, (), 2025.11.03.686349. . PMCID: 12637528.

2.) Kulkarni S, Smith C, Akinniyi OT, Giardine BM, Keller CA, Arnaoutov A, Reese JC (2025 Oct 27). Auxin-induced depletion of human CCR4-NOT subunits reveals opposing functions of CNOT1 and CNOT4 in mRNA metabolism The Journal of Biological Chemistry, 301(12), 110862. . PMCID: 12682128.

3.) Gontu A, Sekhwal MK, Diaz Huemme A, Li L, Kutsaya S, Ling M, Doshi NK, Byukusenge M, Nissly RH (2025 Sep 28). Pasteurized Milk Serves as a Passive Surveillance Tool for Highly Pathogenic Avian Influenza Virus in Dairy Cattle Viruses, 17(10), 1318. . PMCID: 12568113.

4.) Guiltinan MJ, Landherr L, Maximova SN, DelVecchio D, Sebastian A, Albert I (2025 Sep 9). Reduced Susceptibility to Phytophthora in Non-Transgenic Cacao Progeny Through CRISPR-Cas9 Mediated TcNPR3 Mutagenesis. Plant biotechnology journal, (), . doi: 10.1111/pbi.70365. PMID: 40923291.

5.) Ortigas-Vasquez A, Bowen CD, Renner DW, Baigent SJ, Zhang Y, Yao Y, Nair V, Kennedy DA, Szpara ML (2025 Aug 25). High-fidelity long-read sequencing of an avian herpesvirus reveals extensive intrapopulation diversity in tandem repeat regions PLOS Pathogens, 21(8), e1013435. . PMCID: 12425393.

6.) Bresnahan ST, Mahony S, Anton K, Harpur B, Grozinger CM (2025 Jun 18). Intragenomic conflict associated with extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera) Genome Biology, 26(), 171. . PMCID: 12175343.

7.) Lawrence SS, Yamashita H, Shuman L, Raman JD, Joshi M, Yochum GS, Wu XR, Al-Ahmadie HA, Warrick JI, Walter V, DeGraff DJ (2025 May). Interferon-γ/Janus Kinase 1/STAT1 Signaling Represses Forkhead Box A1 and Drives a Basal Transcriptional State in Muscle-Invasive Bladder Cancer. The American journal of pathology, 195(5), 1013-1030. . PMID: 39986350.

8.) Akinniyi OT, Sebastian A, Kulkarni S, Hribal MM, Keller CA, Giardine BM, Albert I, Reese JC (2025 Apr 8). The DNA damage response and RNA Polymerase II regulator Def1 has posttranscriptional functions in the cytoplasm. bioRxiv : the preprint server for biology, (), . . PMID: 39463967.

9.) Ortigas-Vasquez A, Bowen CD, Renner DW, Baigent SJ, Zhang Y, Yao Y, Nair V, Kennedy DA, Szpara ML (2025 Feb 11). High-Fidelity Long-Read Sequencing of an Avian Herpesvirus Reveals Extensive Intrapopulation Diversity in Tandem Repeat Regions bioRxiv, (), 2025.02.10.637388. . PMCID: 11844383.

10.) Chan K, Tseng C, Milarachi E, Goldrich D, Schneper L, Sheldon K, Aliaga C, Alam S, Chatterjee S, El-Bayoumy K, Meyers C, Goldenberg D, Broach JR (2025 Feb 6). Genome Instability Precedes Viral Integration in Human Papillomavirus-Transformed Tonsillar Keratinocytes. Molecular cancer research : MCR, 23(2), 119-127. . PMID: 39475471.

11.) McKinley LN, Bevilacqua PC (2025 Feb). CHiTA: A scarless high-throughput pipeline for characterization of ribozymes. Methods (San Diego, Calif.), 234(), 120-130. . PMID: 39662711.

12.) Rios KT, McGee JP, Sebastian A, Gedara SA, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE (2025 Jan 8). Widespread release of translational repression across Plasmodium’s host-to-vector transmission event PLOS Pathogens, 21(1), e1012823. . PMCID: 11750109.

13.) Nichols RG, Davenport ER (2024 Dec 16). Clade-specific long-read sequencing increases the accuracy and specificity of the gyrB phylogenetic marker gene mSystems, 10(1), e01480-24. . PMCID: 11748558.

14.) Quinlan GM, Hines HM, Grozinger CM (2024 Dec 13). Leveraging Transcriptional Signatures of Diverse Stressors for Bumble Bee Conservation Molecular Ecology, 34(3), e17626. . PMCID: 11754722.

15.) Kulkarni S, Morrissey A, Sebastian A, Giardine B, Smith C, Akinniyi OT, Keller CA, Arnaoutov A, Albert I, Mahony S, Reese JC (2024 Nov 25). Human CCR4-NOT globally regulates gene expression and is a novel silencer of retrotransposon activation. bioRxiv : the preprint server for biology, (), . . PMID: 39314347.

16.) Locatelli NS, Kitchen SA, Stankiewicz KH, Osborne CC, Dellaert Z, Elder H, Kamel B, Koch HR, Fogarty ND, Baums IB (2024 Nov 20). Chromosome-level genome assemblies and genetic maps reveal heterochiasmy and macrosynteny in endangered Atlantic Acropora BMC Genomics, 25(), 1119. . PMCID: 11577847.

17.) Seemiller LR, Goldberg LR, Sebastian A, Siegel SR, Praul C, Zeid D, Albert I, Beierle J, Bryant CD, Gould TJ (2024 Nov). Alcohol and fear conditioning produce strain-specific changes in the dorsal hippocampal transcriptome of adolescent C57BL/6J and DBA/2J mice. Alcohol, clinical & experimental research, 48(11), 2022-2034. doi: 10.1111/acer.15440. PMID: 39279663.

18.) Locatelli NS, Baums IB (2024 Aug 22). Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea bioRxiv, (), 2024.08.21.608299. . PMCID: 11370458.

19.) McKinley LN, Meyer MO, Sebastian A, Chang BK, Messina KJ, Albert I, Bevilacqua PC (2024 Jul 11). Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections. bioRxiv : the preprint server for biology, (), . . PMID: 39026743.

20.) Kulesza E, Thomas P, Prewitt SF, Shalit-Kaneh A, Wafula E, Knollenberg B, Winters N, Esteban E, Pasha A, Provart N, Praul C, Landherr L, dePamphilis C, Maximova SN, Guiltinan MJ (2024 Jun 26). The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L. BMC plant biology, 24(1), 601. . PMID: 38926852.

21.) Pearce DL, Edson JE, Jennelle CS, Walter WD (2024 May 17). Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels Scientific Reports, 14(), 11340. . PMCID: 11101418.

22.) Rios KT, McGee JP, Sebastian A, Moritz RL, Feric M, Absalon S, Swearingen KE, Lindner SE (2024 Feb 1). Global Release of Translational Repression Across Plasmodium’s Host-to-Vector Transmission Event bioRxiv, (), 2024.02.01.577866. . PMCID: 10862809.

Description:

The Genomics Core Facility provides services using several different next-generation sequencing platforms. Applications supported include: Whole-genome and transcriptome sequencing of non-model organisms Amplicon sequencing for metagenomic studies Differential expression analysis of mRNA and miRNA Degradome sequencing ChIP and RIP sequencing