The CoreMarketplace: UF ICBR NextGen DNA Sequencing

Welcome to the UF ICBR NextGen DNA Sequencing core facility. The ICBR-NGS core provides researchers with quality, massively parallel, high-throughput sequencing data using the most current instrumentation, at a reasonable cost. We currently support the most popular platforms: Illumina NextSeq500 and MiSeq, HiSeq3000 and the Pacific Biosciences SEQUEL system. Together, these instruments cover a broad range of powerful applications. Our free consultation services aim to help researchers navigate through the complex matrix of experimental options represented by the available sequencing technologies. Some of these important considerations include: read length, error rate, predominant type of error, data output/run, speed, cost, etc. The ever-broadening range of applications include (but are not limited to) de novo sequencing of whole genomes, targeted sequencing, transcriptome sequencing (RNA-Seq), chromatin immunoprecipitation (ChIP) sequencing, methylation analysis and metagenomics.

Our sample prep and library construction services are offered through both the NGS and the GeneExpression/Genotyping Cores. Please contact us if the service of your interest is not listed. We strive to support most common applications.

Facility Policies

Services are offerred outside of University of Florida

Consulting is offerred outside of University of Florida

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Services offered:

10x Genomics

DNA Analysis

Library Services

Metagenomics Analysis

RNA analysis

RNAseq

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Facility Equipment

2100 Bioanalyzer Instrument

The 2100 Bioanalyzer system is an automated electrophoresis tool that provides precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use. [Product Link]

RRID:SCR_018043

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Agilent 4200 Tapestation Genetic Analyzer

Benchtop genetic analyzer electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow. [Product Link]

RRID:SCR_018435

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10x Genomics Chromium
Agilent Tapestation 2200
Bio-Rad C1000 Touch Thermocycler
BMG Labtech Fluostar Omega
Covaris E220
Covaris S220
Illumina iSeq
Illumina MiSeq
Illumina NextSeq 500
Illumina NovaSeq 6000
PacBio Sequel
Sage ELF
Invitrogen Qubit 3.0

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Publications

Publications associated with this facility (Click To View):

1.) Ketchum RN, Smith EG, Toledo LM, Leach WB, Padillo-Anthemides N, Baxevanis AD, Reitzel AM, Ryan JF (2024 Nov 9). Rapid speciation in the holopelagic ctenophore Mnemiopsis following glacial recession bioRxiv, (), 2024.10.10.617593. . PMCID: 11580945.

2.) 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.

3.) 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.

4.) 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.

5.) Markee A, Godfrey RK, Frandsen PB, Weng YM, Triant DA, Kawahara AY (2024 Jul 3). De Novo Long-Read Genome Assembly and Annotation of the Luna Moth (Actias luna) Fully Resolves Repeat-Rich Silk Genes Genome Biology and Evolution, 16(7), evae148. . PMCID: 11258402.

6.) 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.

7.) 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.

8.) Barbosa M, Lefler FW, Berthold DE, Gettys LA, Leary JK, Laughinghouse HD 4th (2024 May 1). Macrophyte coverage drives microbial community structure and interactions in a shallow sub-tropical lake. The Science of the total environment, 923(), 171414. doi: 10.1016/j.scitotenv.2024.171414. PMID: 38442760.

9.) 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.

10.) 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.

11.) Lefler FW, Barbosa M, Berthold DE, Roten R, Bishop WM, Laughinghouse HD IV (2024 Apr 26). Microbial Community Response to Granular Peroxide-Based Algaecide Treatment of a Cyanobacterial Harmful Algal Bloom in Lake Okeechobee, Florida (USA) Toxins, 16(5), 206. . PMCID: 11125911.

12.) McGrath-Blaser SE, McGathey N, Pardon A, Hartmann AM, Longo AV (2024 Apr 17). Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens Proceedings of the Royal Society B: Biological Sciences, 291(2021), 20232658. . PMCID: 11021929.

13.) Atanasova KR, Perkins CM, Ratnayake R, Jiang J, Chen QY, Schmittgen TD, Luesch H (2024 Mar 6). Epigenetic small-molecule screen for inhibition and reversal of acinar ductal metaplasia in mouse pancreatic organoids Frontiers in Pharmacology, 15(), 1335246. . PMCID: 10953826.

14.) Poulos MG, Ramalingam P, Winiarski A, Gutkin MC, Katsnelson L, Carter C, Pibouin-Fragner L, Eichmann A, Thomas JL, Miquerol L, Butler JM (2024 Mar 4). Complementary and Inducible creERT2 Mouse Models for Functional Evaluation of Endothelial Cell Subtypes in the Bone Marrow Stem Cell Reviews and Reports, 20(4), 1135-1149. . PMCID: 11087254.

15.) Skojec C, Godfrey RK, Kawahara AY (2024 Feb 7). Long read genome assembly of Automeris io (Lepidoptera: Saturniidae) an emerging model for the evolution of deimatic displays G3: Genes|Genomes|Genetics, 14(3), jkad292. . PMCID: 10917498.

16.) Murray KO, Brant JO, Spradlin RA, Thome T, Laitano O, Ryan TE, Riva A, Kladde MP, Clanton TL (2024 Feb 1). Exertional heat stroke causes long-term skeletal muscle epigenetic reprogramming, altered gene expression, and impaired satellite cell function in mice. American journal of physiology. Regulatory, integrative and comparative physiology, 326(2), R160-R175. doi: 10.1152/ajpregu.00226.2023. PMID: 38047316.

17.) 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.

18.) 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.

19.) 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.

20.) 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.

21.) 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.

22.) Mosby CA, Long KJ, Phillips MB, Bartel J, Jones MK (2023 Dec 16). Changes in the Murine Microbiome and Bacterial Extracellular Vesicle Production in Response to Antibiotic Treatment and Norovirus Infection Viruses, 15(12), 2443. . PMCID: 10747002.

23.) Kalkreuter E, Kautsar SA, Yang D, Teijaro CN, Bader CD, Fluegel LL, Davis CM, Simpson JR, Steele AD, Gui C, Meng S, Li G, Viehrig K, Ye F, Su P, Kiefer AF, Lauterbach L, Nichols A, Cepeda AJ, Yan W, Fan B, Jiang Y, Adhikari A, Zheng CJ, Shen B (2023 Dec 15). The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity bioRxiv, (), 2023.12.14.571759. . PMCID: 10760148.

24.) Atanasova KR, Perkins CM, Ratnayake R, Jiang J, Chen QY, Schmittgen TD, Luesch H (2023 Nov 27). Epigenetic Small-Molecule Screen for Inhibition and Reversal of Acinar Ductal Metaplasia in Mouse Pancreatic Organoids. bioRxiv : the preprint server for biology, (), . . PMID: 38077007.

25.) Howard RD, Schul MD, Rodriguez Bravo LM, Altieri AH, Meyer JL (2023 Nov 2). Shifts in the coral microbiome in response to in situ experimental deoxygenation Applied and Environmental Microbiology, 89(11), e00577-23. . PMCID: 10686059.

26.) 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.

27.) 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.

28.) 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.

29.) Foresman D, Tartar A (2023 Oct 16). The transcriptome of the entomopathogenic fungus Culicinomyces clavisporus contains an ortholog of the insecticidal ribotoxin Hirsutellin PeerJ, 11(), e16259. . PMCID: 10586291.

30.) Kondratov O, Zolotukhin S (2023 Sep 23). Exploring the Comprehensive Kozak Sequence Landscape for AAV Production in Sf9 System Viruses, 15(10), 1983. . PMCID: 10612025.

31.) Parafati M, Giza S, Shenoy TS, Mojica-Santiago JA, Hopf M, Malany LK, Platt D, Moore I, Jacobs ZA, Kuehl P, Rexroat J, Barnett G, Schmidt CE, McLamb WT, Clements T, Coen PM, Malany S (2023 Sep 15). Human skeletal muscle tissue chip autonomous payload reveals changes in fiber type and metabolic gene expression due to spaceflight NPJ Microgravity, 9(), 77. . PMCID: 10504373.

32.) Schul MD, Anastasious DE, Spiers LJ, Meyer JL, Frazer TK, Brown AL (2023 Jun 21). Concordance of microbial and visual health indicators of white-band disease in nursery reared Caribbean coral Acropora cervicornis PeerJ, 11(), e15170. . PMCID: 10290447.

33.) Godfrey RK, Britton SE, Mishra S, Goldberg JK, Kawahara AY (2023 Apr 29). A high-quality, long-read genome assembly of the whitelined sphinx moth (Lepidoptera: Sphingidae: Hyles lineata) shows highly conserved melanin synthesis pathway genes G3: Genes|Genomes|Genetics, 13(6), jkad090. . PMCID: 10234378.

34.) Morgan WR, Tartar A (2023 Apr 13). Decontamination and Annotation of the Draft Genome Sequence of the Oomycete Lagenidium giganteum ARSEF 373 Microbiology Resource Announcements, 12(5), e01346-22. . PMCID: 10190603.

35.) Meyer JL, Gunasekera SP, Brown AL, Ding Y, Miller S, Teplitski M, Paul VJ (2023 Jan 22). Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics Marine Drugs, 21(2), 76. . PMCID: 9967302.

36.) Wolff CA, Gutierrez-Monreal MA, Meng L, Zhang X, Douma LG, Costello HM, Douglas CM, Ebrahimi E, Pham A, Oliveira AC, Fu C, Nguyen A, Alava BR, Hesketh SJ, Morris AR, Endale MM, Crislip GR, Cheng KY, Schroder EA, Delisle BP, Bryant AJ, Gumz ML, Huo Z, Liu AC, Esser KA (2023 Jan 9). Defining the age-dependent and tissue-specific circadian transcriptome in male mice Cell reports, 42(1), 111982. . PMCID: 9929559.

37.) 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.

38.) 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.

39.) Sosa F, Carmickle AT, Oliveira LJ, Sagheer M, Saleem M, Yu FH, Altman MD, Dikmen S, Denicol AC, Sonstegard TS, Larson CC, Hansen PJ (2022 Nov). Effects of the bovine SLICK1 mutation in PRLR on sweat gland area, FOXA1 abundance, and global gene expression in skin. Journal of dairy science, 105(11), 9206-9215. doi: 10.3168/jds.2022-22272. PMID: 36085108.

40.) 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.

41.) 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.

42.) 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.

43.) 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.

44.) 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 Jr, Lauzardo M, Prosperi M, Salemi M (2022 Mar 10). 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. . PMCID: 9617581.

45.) 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.

46.) 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.

47.) 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.

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Associations

ABRF

Association of Biomolecular Resource Facilities

SEASR

Southeastern Association of Shared Resources

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Metadata

Links

All the links listed resolve to this core profile

https://coremarketplace.org/?FacilityID=650
https://coremarketplace.org/RRID:SCR_019152

Institution

Institution ROR ID: https://ror.org/02y3ad647

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Keywords:

USEDit, sequencing technologies, de novo sequencing, whole genomes, targeted sequencing, transcriptome sequencing, chromatin immunoprecipitation sequencing, methylation analysis, metagenomics, ABRF, ABRF

Resource Type:

core facility, service resource, access service resource

Citation:

University of Florida ICBR NextGen DNA Sequencing Core Facility (RRID:SCR_019152)

UF ICBR NextGen DNA Sequencing (Sequencing)

Facility LIMS Page

Primary Contact:

Facility RRID

Facility Details

Facility Policies

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Services offered:

Facility Equipment

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Publications

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Associations

ABRF

SEASR

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Metadata

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Facility Profile QR Code (links to this profile)

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Contact Edith "Angel" Sampson

Contact The CoreMarketplace

UF ICBR NextGen DNA Sequencing

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