University of Florida
Edith "Angel" Sampson
2033 Mowry Road
CGRC 178
Gainesville, FL 32610
https://biotech.ufl.edu/gene-expression-genotyping/
RRID: RRID:SCR_019145
Bio-Rad CFX96 Real-Time PCR Detection System
The CFX96 Touch System is a real-time PCR detection system that combines optical technology with temperature control. This six-channel (five colors and one FRET channel) real-time PCR instrument combines advanced optical technology with precise temperature control to deliver sensitive, reliable detection for singlexplex or multiplex reactions. Quickly set up runs and monitor amplification traces in real time on the integrated LCD touch screen, or use the included CFX Maestro Software to easily and intuitively design your experiment and analyze results from a connected computer. With up to five-target detection, thermal cycler performance, unrivaled stand-alone functionality, and easy-to-use software, the CFX96 Touch System is designed to advance your qPCR. [Product Link]
RRID:SCR_018064
Nanodrop 8000 Spectrophotometer
Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. It can analyze spectrum of 220nm to 750nm. [Product Link]
RRID:SCR_018600
10x Genomics (Chromium)
Agilent 2100 Bioanalyzer
Agilent Bravo Platform
Bio-Rad QX200 Digital PCR System
GeneChip Hybridization Oven 640
GeneChip Scanner 3000 7G
Thermo Fisher 3730XL DNA Analyzer
10x Genomics
Antibody Sequencing
Consultations
CRISPR Rosa26 & CRISPR H11
CRISPR/Cas Project Design
Data Analysis
Digital PCR
DNA Analysis
Droplet Digital PCR
ELISA
Gene Expression Arrays
Genome/Transcriptome Assembly And Annotation
Genomics
Genotyping
Library Services
Molecular Library Services
PCR Arrays
Protein Extraction/Purification
Reagents
Real-time qPCR
RNA analysis
RNA Integrity
RNA Isolation
RNAseq
Single-Cell Analysis
Single-cell Sequencing
1.) Luo YE, Abe-Teh Z, Alsaghir T, Heiden KD, Basso KB, Barton ER (2026 Mar 31). Fibro-adipogenic progenitor cells from murine SMA muscles are intrinsically adipogenic. Proceedings of the National Academy of Sciences of the United States of America, 123(13), e2525423123. . PMCID: 13037897.
2.) Tantawy M, Wang D, Gbadamosi M, Yu F, Zhang Y, Alomar ME, Shain KH, Baz RC, Bruno KA, Gong Y (2026 Feb). Atorvastatin Protects Against Deleterious Carfilzomib-Induced Transcriptional Changes in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. International Journal of Molecular Sciences, 27(3), . . PMCID: 12898222.
3.) Montalvo RN, Nguyen BL, Doerr V, Dowllah IM, Wendler CC, Baumfalk DR, Babuschak JC, Krueger RW, Smuder AJ (2026 Jan 1). Sex Differences in Response to Acute Doxorubicin Cardiorespiratory Muscle Dysfunction and Preconditioning Exercise. Medicine and science in sports and exercise, 58(1), 47-59. . PMCID: 12911280.
4.) Seo D, Strickland HF, Zhou M, Barker R, Ferl RJ, Paul AL, Gilroy S (2025 Oct 28). GLARE: discovering hidden patterns in spaceflight transcriptome using representation learning. NPJ microgravity, 11(1), 76. . PMCID: 12569054.
5.) Kolling FW, Podnar JW, Wilkins O, Fraser CJ, MacDonald ML, Polson SW, Herbert ZT, Chittur SV, Hayden A, Kuentzel M, Heinz M, Huerta GM, Stevenson HS, Karmakar A, Fronick C, Cook L, Vargas S, Xuei X, McGuire P, Zeller M, Zhang Y, Dai R, Wang X, Wai CM, Thimmapuram J, Arora D, Mesa T, Fan J, Alekseyev YO, Cervone F, Williams C, Gorham N, Lemenze A, Goodwin S, Preall J, Whittaker CA (2025 Oct 24). Multi-site Assessment of Methods for Cell Preservation Upstream of Single Cell RNA Sequencing. bioRxiv : the preprint server for biology, (), . . PMCID: 12633272.
6.) Chitre S, Gharaibeh RZ, Jobin C (2025 Sep 23). A defined bacterial consortium and spatial transcriptomics highlight the complex interaction between Campylobacter jejuni and the murine intestine. bioRxiv : the preprint server for biology, (), . . PMID: 41040308.
7.) Madrid G, Raimundo GA, Reyes FA, Picoli EA, Resende Jr. MF, Balmant KM (2025 Sep 10). An improved nuclei isolation protocol from leaf tissue for single-cell transcriptomics PLOS One, 20(9), e0302118. . PMCID: 12422464.
8.) Sieber KR, Saar M, Newell N, Fernandez K, Franco FP, Sujimoto FR, Francoeur CB, Pereira RM, Currie CR, Simões Bento JM, Yan H (2025 Aug 24). Caste- and environment-associated differential expression of olfactory receptors in pest ants Scientific Reports, 15(), 31079. . PMCID: 12375091.
9.) Laforest LC, Nguyen TA, Matsumoto GO, Ramachandria P, Chanderbali A, Kanumuri SR, Sharma A, McCurdy CR, Dang TT, Nadakuduti SS (2025 Aug 18). A chromosome-level Mitragyna parvifolia genome unveils spirooxindole alkaloid diversification and mitraphylline biosynthesis The Plant Cell, 37(9), koaf207. . PMCID: 12419693.
10.) Scott KA, Eikenberry SA, Elsaafien K, Baumer-Harrison C, Johnson DN, Sá JM, Bartolomucci A, Sumners C, Krause EG, de Kloet AD (2025 Aug 13). Cardiometabolic and anxiogenic consequences of chronic social defeat stress in male mice Neurobiology of Stress, 38(), 100752. . PMCID: 12489766.
11.) Taboada VP, Wu Y, Cassidy R, Medvedev KE, Loeff L, Nemudraia A, Nemudryi A (2025 Jul 24). Bacterial Schlafens mediate anti-phage defense bioRxiv, (), 2025.07.24.666596. . PMCID: 12330615.
12.) Bogale M, Sampson E, Hu W, Baniya A, Mishra S, Kwon K, Lopez-Nicora HD, DiGennaro P (2025 Jul 19). Development of Monoclonal Antibodies for Identifying Plant-Parasitic Nematodes Journal of Nematology, 57(1), 20250024. . PMCID: 12275506.
13.) Dill MN, Turner Z, Kapuscinska PW, Heiden K, Basso KB, Simmons CS, Moore E (2025 Jun 9). Exploring the Unique Extracellular Matrix Composition of Acomys as a Potential Key to Resisting Fibrosis. ACS biomaterials science & engineering, 11(6), 3616-3633. doi: 10.1021/acsbiomaterials.5c00810. PMID: 40407745.
14.) Duran-Pinedo A, Solbiati JO, Teles F, Yanping Z, Frias-Lopez J (2025 May 14). Longitudinal host-microbiome dynamics of metatranscription identify hallmarks of progression in periodontitis. Microbiome, 13(1), 119. . PMID: 40369640.
15.) Diedrick WA, Kanga LH, Mallinger R, Pescador M, Elsharkawy I, Zhang Y (2025 Apr 2). Molecular Assessment of Genes Linked to Honeybee Health Fed with Different Diets in Nuclear Colonies Insects, 16(4), 374. . PMCID: 12027810.
16.) Enriquez V, Munzen ME, Porras LM, Charles-Niño CL, Yu F, Alviña K, Ramos RL, Dores MR, Giusti-Rodriguez P, Martinez LR (2025 Mar 4). Active Cryptococcus neoformans glucuronoxylomannan production prevents elimination of cryptococcal CNS infection in vivo. Journal of neuroinflammation, 22(1), 61. . PMID: 40038673.
17.) Gurgel BCV, Vilela N, Soares KH, Juliasse LER, Aukhil I, Duarte PM (2025). Comprehensive analysis of transcriptome and pathway interactions in periodontitis. Journal of applied oral science : revista FOB, 33(), e20250396. . PMCID: 12677198.
18.) Lin C-Y, Robledo Buritica J, Sarkar P, Jassar O, Rocha SV, Batuman O, Stelinski LL, Levy A (2024 Dec 23). An insect virus differentially alters gene expression among life stages of an insect vector and enhances bacterial phytopathogen transmission. Journal of virology, (), e0163024. doi: 10.1128/jvi.01630-24. PMID: 39714167.
19.) Gutierrez-Monreal MA, Wolff CA, Rijos EE, Viggars MR, Douglas CM, Pagala V, Peng J, Hunt LC, Ding H, Huo Z, Demontis F, Esser KA (2024 Oct 1). Targeted Bmal1 restoration in muscle prolongs lifespan with systemic health effects in aging model JCI Insight, 9(22), e174007. . PMCID: 11601919.
20.) Brinley AR, Conner PJ, Yu F, Sarkhosh A, Liu T (2024 Oct). Morphological and genetic characterization of the muscadine fruit abscission zone. Horticulture research, 11(10), uhae227. . PMID: 39415976.
21.) Ghayee HK, Costa KA, Xu Y, Hatch HM, Rodriguez M, Straight SC, Bustamante M, Yu F, Smagulova F, Bowden JA, Tevosian SG (2024 Sep 18). Polyamine Pathway Inhibitor DENSPM Suppresses Lipid Metabolism in Pheochromocytoma Cell Line International Journal of Molecular Sciences, 25(18), 10029. . PMCID: 11432427.
22.) Pelosi JA, Davenport R, Barbazuk WB, Sessa EB, Kuo L (2024 Sep 5). An efficient and effective RNA extraction protocol for ferns Applications in Plant Sciences, 12(6), e11617. . PMCID: 11610414.
23.) Zhou M, Ferl RJ, Paul AL (2024 Aug 6). Light has a principal role in the Arabidopsis transcriptomic response to the spaceflight environment NPJ Microgravity, 10(), 82. . PMCID: 11303767.
24.) Jin Z, De U, Tithi TI, Kleberg J, Nataraj A, Jolley E, Carelock ME, Davies BS, Zhang W, Kolb R (2024 Aug 1). ANGPTL4 Suppresses Clear Cell Renal Cell Carcinoma via Inhibition of Lysosomal Acid Lipase. Cancer research communications, 4(8), 2242-2254. . PMID: 39105498.
25.) Kokkaliari S, Grauso L, Mangoni A, Seabra G, Paul VJ, Luesch H (2024 Jul 18). Isolation, Structure Elucidation, and Biological Activity of the Selective TACR2 Antagonist Tumonolide and its Aldehyde from a Marine Cyanobacterium Chemistry (Weinheim an der Bergstrasse, Germany), 30(50), e202401393. . PMCID: 12051037.
26.) Kok HJ, Fletcher DB, Oster JC, Conover CF, Barton ER, Yarrow JF (2024 May 19). Transcriptomics reveals transient and dynamic muscle fibrosis and atrophy differences following spinal cord injury in rats Journal of Cachexia, Sarcopenia and Muscle, 15(4), 1309-1323. . PMCID: 11294049.
27.) Romero-Carramiñana I, Dominguez-Zorita S, Esparza-Moltó PB, Cuezva JM (2024 May 3). Ablation of Atp5if1 impairs metabolic reprogramming and proliferation of T lymphocytes and compromises mouse survival iScience, 27(6), 109863. . PMCID: 11126974.
28.) Zhou M, Riva A, Gauthier ML, Kladde MP, Ferl RJ, Paul AL (2024 Apr 30). Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight. Biology direct, 19(1), 33. . PMID: 38689301.
29.) Viggars MR, Berko HE, Hesketh SJ, Wolff CA, Gutierrez-Monreal MA, Martin RA, Jennings IG, Huo Z, Esser KA (2024 Apr 27). Skeletal muscle BMAL1 is necessary for transcriptional adaptation of local and peripheral tissues in response to endurance exercise training. bioRxiv : the preprint server for biology, (), . . PMID: 37905004.
30.) Sobh A, Encinas E, Patel A, Surapaneni G, Bonilla E, Kaestner C, Poullard J, Clerio M, Vasan K, Freeman T, Lv D, Dupéré-Richer D, Riva A, Barwick BG, Zhou D, Boise LH, Mitsiades CS, Kim B, Bennett RL, Chandel NS, Licht JD (2024 Apr 12). NSD2 drives t(4;14) myeloma cell dependence on adenylate kinase 2 by diverting one-carbon metabolism to the epigenome Blood, 144(3), 283-295. . PMCID: 11830969.
31.) Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan LB, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD (2024 Mar). The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals Genome Research, 34(3), 498-513. . PMCID: 11067881.
32.) Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ (2024 Feb 19). The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor Communications Biology, 7(), 203. . PMCID: 10876535.
33.) Poole B, Oshins R, Huo Z, Aranyos A, West J, Duarte S, Clark VC, Beduschi T, Zarrinpar A, Brantly M, Khodayari N (2024 Jan 29). Sirtuin3 promotes the degradation of hepatic Z alpha-1 antitrypsin through lipophagy Hepatology Communications, 8(2), e0370. . PMCID: 10830086.
34.) Marini S, Huber A, Cash MN, Salemi M, Cook RL, Borsa P, Mavian CN (2024 Jan 22). Oral Cannabidiol Treatment Is Associated with an Anti-Inflammatory Gene Expression Signature in Myeloid Cells of People Living with HIV. Cannabis and cannabinoid research, (), . doi: 10.1089/can.2023.0139. PMID: 38252549.
35.) Duarte PM, Gurgel BCV, Miranda TS, Sardenberg J, Gu T, Aukhil I (2024). Distinctive genes and signaling pathways associated with type 2 diabetes-related periodontitis: Preliminary study. PloS one, 19(1), e0296925. . PMID: 38241313.
36.) Febres VJ, Fadli A, Meyering B, Yu F, Bowman KD, Chaparro JX, Albrecht U (2024). Dissection of transcriptional events in graft incompatible reactions of "Bearss" lemon (Citrus limon) and "Valencia" sweet orange (C. sinensis) on a novel citrandarin (C. reticulata × Poncirus trifoliata) rootstock. Frontiers in plant science, 15(), 1421734. . PMID: 38966146.
37.) Ferl RJ, Zhou M, Strickland HF, Haveman NJ, Callaham JB, Bandla S, Ambriz D, Paul AL (2023 Dec 20). Transcriptomic dynamics in the transition from ground to space are revealed by Virgin Galactic human-tended suborbital spaceflight NPJ Microgravity, 9(), 95. . PMCID: 10733374.
38.) Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA (2023 Nov 6). Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. The Journal of experimental medicine, 220(11), . . PMID: 37615936.
39.) Li Q, Zhou M, Chhajed S, Yu F, Chen S, Zhang Y, Mou Z (2023 Oct 27). N-hydroxypipecolic acid triggers systemic acquired resistance through extracellular NAD(P) Nature Communications, 14(), 6848. . PMCID: 10611778.
40.) Al-Awadhi FH, Simon EF, Liu N, Ratnayake R, Paul VJ, Luesch H (2023 Oct 25). Discovery and Anti-Inflammatory Activity of a Cyanobacterial Fatty Acid Targeting the Keap1/Nrf2 Pathway Marine Drugs, 21(11), 553. . PMCID: 10672429.
41.) Viggars MR, Berko HE, Gutierrez-Monreal MA, Martin RA, Esser KA (2023 Oct 17). Muscle Bmal1 is necessary for normal transcriptomic and metabolomic adaptation to endurance exercise training bioRxiv, (), 2023.10.13.562100. . PMCID: 10614785.
42.) Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan L, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD (2023 Aug 27). The genome of the colonial hydroid Hydractinia reveals their stem cells utilize a toolkit of evolutionarily shared genes with all animals bioRxiv, (), 2023.08.25.554815. . PMCID: 10541594.
43.) Olanrewaju GO, Haveman NJ, Naldrett MJ, Paul AL, Ferl RJ, Wyatt SE (2023). Integrative transcriptomics and proteomics profiling of Arabidopsis thaliana elucidates novel mechanisms underlying spaceflight adaptation. Frontiers in plant science, 14(), 1260429. . PMID: 38089794.
44.) Haveman NJ, Zhou M, Callaham J, Strickland HF, Houze D, Manning-Roach S, Newsham G, Paul AL, Ferl RJ (2022 Nov 13). Utilizing the KSC Fixation Tube to Conduct Human-Tended Plant Biology Experiments on a Suborbital Spaceflight Life, 12(11), 1871. . PMCID: 9693084.
45.) Rife Magalis B, Rich S, Tagliamonte MS, Mavian C, Cash MN, Riva A, Marini S, Amador DM, Zhang Y, Shapiro J, Horine A, Starostik P, Pieretti M, Vega S, Paula Lacombe A, Salinas J, Stevenson M, Myers P, Glenn Morris J, Lauzardo M, Prosperi M, Salemi M (2022 Oct 29). Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 75(9), 1618-1627. . PMID: 35271704.
46.) Prías-Blanco M, Chappell TM, Freed EF, Illa-Berenguer E, Eckert CA, Parrott WA (2022 Oct 14). An Agrobacterium strain auxotrophic for methionine is useful for switchgrass transformation Transgenic Research, 31(6), 661-676. . PMCID: 9747830.
47.) Gu W, Madrid DMC, Joyce S, Driver JP (2022 Jul 5). A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs. Cell reports, 40(1), 111050. . PMID: 35793622.
48.) Paul AL, Elardo SM, Ferl R (2022 May 12). Plants grown in Apollo lunar regolith present stress-associated transcriptomes that inform prospects for lunar exploration Communications Biology, 5(), 382. . PMCID: 9098553.
49.) Magalis BR, Mavian C, Tagliamonte M, Rich SN, Cash M, Riva A, Loeb JC, Norris M, Amador DM, Zhang Y, Shapiro J, Starostik P, Marini S, Myers P, Ostrov DA, Lednicky JA, Glenn Morris J Jr, Lauzardo M, Salemi M (2022 Apr 13). Low‐frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled‐edged sword Journal of Medical Virology, 94(7), 3192-3202. . PMCID: 9325371.
50.) De Maria M, Kroll KJ, Yu F, Nouri MZ, Silva-Sanchez C, Perez JG, Moraga D, Zhang Y, Walsh MT, Denslow ND (2022 Mar 12). Endocrine, immune and renal toxicity in male largemouth bass after chronic exposure to glyphosate and Rodeo® Aquatic toxicology (Amsterdam, Netherlands), 246(), 106142. . PMCID: 9007883.
51.) Nguyen LT, Macaluso NC, Pizzano BLM, Cash MN, Spacek J, Karasek J, Miller MR, Lednicky JA, Dinglasan RR, Salemi M, Jain PK (2022 Mar). A thermostable Cas12b from Brevibacillus leverages one-pot discrimination of SARS-CoV-2 variants of concern. EBioMedicine, 77(), 103926. . PMID: 35290826.
52.) Paul AL, Haveman N, Califar B, Ferl RJ (2021 Sep 13). Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis Frontiers in Plant Science, 12(), 691790. . PMCID: 8475764.
53.) Paul AL, Haveman N, Califar B, Ferl RJ (2021). Epigenomic Regulators Elongator Complex Subunit 2 and Methyltransferase 1 Differentially Condition the Spaceflight Response in Arabidopsis. Frontiers in plant science, 12(), 691790. doi: 10.3389/fpls.2021.691790. PMID: 34589093.
54.) Narusaka M, Kubo Y, Hatakeyama K, Imamura J, Ezura H, Nanasato Y, Tabei Y, Takano Y, Shirasu K, Narusaka Y (2013). Interfamily transfer of dual NB-LRR genes confers resistance to multiple pathogens. PloS one, 8(2), e55954. doi: 10.1371/journal.pone.0055954. PMID: 23437080.
The Gene Expression & Genotyping core provides state-of-the-art technical services and consultation on Single Cell RNA-Seq, RNA-Seq, 16s metagenomics and Affymetrix gene expression arrays. High-throughput RNA-seq libraries, 16s libraries and sequencing capture libraries can be done by using the Agilent Bravo robot. QuantiGene RNA Assays measure up to 80 gene targets directly with degraded and cross-linked RNA in FFPE tissues and blood, with no RNA purification required. The BioRad QX200 AutoDG Droplet Digital PCR System provides absolute quantification of target DNA or RNA molecules with greater precision and sensitivity than qPCR, the sensitivity off ddPCR System can facilitate expanded analysis of single cells. The Genotyping services include fragment analysis using AB3730 (96 capillary technology), development of microsatellite libraries using Illumina sequence data, and genotyping using mouse tails or ear punches. These up-to-date gene expression and genotyping analysis methods allow scientists to be on the cutting edge of research.
