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SDState-Genomics Sequencing Facility (Genomics / Genome Analysis and Technologies)

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2380 Research Parkway

Brookings, SD 57006

United States

https://www.sdstate.edu/genomics-sequencing-facility

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Quicklinks:

https://www.coremarketplace.org/SDStateG https://www.coremarketplace.org/RRID:SCR_023959

Primary Contact:

Jose Gonzalez

Last Updated: 05/19/2025

Facility RRID

RRID:SCR_023959

Facility Details

The SDState Genomics Sequencing Facility offers custom sequencing services from DNA/RNA extractions to sequencing using Illumina and Oxford Nanopore platforms. Projects examples include bulk RNAseq, 3‘RNASeq, Single Cell transcriptomics (10X Genomics), Genome sequencing, and amplicon sequencing (ie 16SRNA, genotyping).
We can also partner with you for experimental design and bioinformatics data analysis.

Facility Policies

Services are offerred outside of South Dakota State University

Consulting is offerred outside of South Dakota State University

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Services offered:

10x Genomics

DNA Analysis

DNA Isolation

Genome/Transcriptome Assembly And Annotation

Genomics

Genotyping

Genotyping-by-sequencing

Long Read Amplicon Sequencing

Long Read Sequencing

Metagenomics Analysis

Metatranscriptomics

Microbiome

Nanopore Sequencing

Reduce Representation Methylation Sequencing

RNA-Seq Training

RNAseq

Sample Preparation

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Single-cell Sequencing

Whole Genome Sequencing

Facility Equipment

Illumina MiSeq System

Access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 Ã— 300 bp read lengths. [Product Link]

RRID:SCR_020134

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Illumina NextSeq 550 System

With tunable output and high data quality, it provides flexible power you need for whole genome, transcriptome, and targeted resequencing plus ability to scan microarrays including Infinium MethylationEPIC BeadChip and other select BeadChips. [Product Link]

RRID:SCR_020141

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Oxford Nanopore Promethion P2 Solo

Long reads sequencer

No additional equipment has been listed

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Publications

Publications associated with this facility (Click To View):

1.) Wollman J, Wanniarachchi K, Pradhan B, Huang L, Kerkvliet JG, Hoppe AD, Thiex NW (2024 Nov 21). Mannose receptor (MRC1) mediates uptake of dextran by bone marrow–derived macrophages Molecular Biology of the Cell, 35(12), ar153. . PMCID: 11656472.

2.) Wollman J, Wanniarachchi K, Pradhan B, Huang L, Kerkvliet JG, Hoppe AD, Thiex NW (2024 Aug 13). Mannose receptor (MRC1) mediates uptake of dextran in macrophages via receptor-mediated endocytosis. bioRxiv : the preprint server for biology, (), . . PMID: 39211167.

3.) Alhusays A, Galvin C, Torres M, Sengar M, Fitzpatrick E, Gonzalez Hernandez JLL, Glover KD, Solanki S, Ameen G (2024 Jul 9). First Report of Pantoea ananatis causing leaf streak disease on wheat (Triticum aestivum) in the United States of America. Plant disease, (), . doi: 10.1094/PDIS-04-24-0903-PDN. PMID: 38982676.

4.) Kovács AD, Gonzalez Hernandez JL, Pearce DA (2023 Nov 6). Acidified drinking water improves motor function, prevents tremors and changes disease trajectory in Cln2(R207X) mice, a model of late infantile Batten disease. Scientific reports, 13(1), 19229. . ID: 37932327.

5.) Adachi H, Sakai T, Kourelis J, Pai H, Gonzalez Hernandez JL, Utsumi Y, Seki M, Maqbool A, Kamoun S (2023 Sep 27). Jurassic NLR: Conserved and dynamic evolutionary features of the atypically ancient immune receptor ZAR1. The Plant cell, 35(10), 3662-3685. . ID: 37467141.

6.) Gupta R, Khan MIR, Gonzalez Hernandez JL, Wang W, Bindschedler LV (2022). Editorial: Improvement of Rice Through "-omics" Approaches. Frontiers in plant science, 13(), 926976. . ID: 35685014.

7.) Aljutaily T, Huarte E, Martinez-Monteagudo S, Gonzalez-Hernandez JL, Rovai M, Sergeev IN (2020 Oct). Probiotic-enriched milk and dairy products increase gut microbiota diversity: a comparative study. Nutrition research (New York, N.Y.), 82(), 25-33. doi: 10.1016/j.nutres.2020.06.017. ID: 32949953.

8.) Bruggeman SA, Horvath DP, Fennell AY, Gonzalez-Hernandez JL, Clay SA (2020). Teosinte (Zea mays ssp parviglumis) growth and transcriptomic response to weed stress identifies similarities and differences between varieties and with modern maize varieties. PloS one, 15(8), e0237715. . ID: 32822374.

9.) Chaichi M, Sanjarian F, Razavi K, Gonzalez-Hernandez JL (2019). Analysis of transcriptional responses in root tissue of bread wheat landrace (Triticum aestivum L.) reveals drought avoidance mechanisms under water scarcity. PloS one, 14(3), e0212671. . ID: 30840683.

10.) Ma Q, Bücking H, Gonzalez Hernandez JL, Subramanian S (2019). Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities. Frontiers in microbiology, 10(), 2452. . ID: 31736899.

11.) Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK (2018). Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. Frontiers in plant science, 9(), 926. . ID: 30034404.

12.) Paudel B, Das A, Tran M, Boe A, Palmer NA, Sarath G, Gonzalez-Hernandez JL, Rushton PJ, Rohila JS (2016). Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. Frontiers in plant science, 7(), 293. . ID: 27014316.

13.) Graves H, Rayburn AL, Gonzalez-Hernandez JL, Nah G, Kim DS, Lee DK (2015). Validating DNA Polymorphisms Using KASP Assay in Prairie Cordgrass (Spartina pectinata Link) Populations in the U.S. Frontiers in plant science, 6(), 1271. . ID: 26834772.

14.) Gedye KR, Gonzalez-Hernandez JL, Owens V, Boe A (2012). Advances towards a Marker-Assisted Selection Breeding Program in Prairie Cordgrass, a Biomass Crop. International journal of plant genomics, 2012(), 313545. . ID: 23227036.

15.) Rosyara UR, Gonzalez-Hernandez JL, Glover KD, Gedye KR, Stein JM (2009 May). Family-based mapping of quantitative trait loci in plant breeding populations with resistance to Fusarium head blight in wheat as an illustration. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 118(8), 1617-31. doi: 10.1007/s00122-009-1010-9. ID: 19322557.

16.) Singh PK, Gonzalez-Hernandez JL, Mergoum M, Ali S, Adhikari TB, Kianian SF, Elias EM, Hughes GR (2006 Aug). Identification and Molecular Mapping of a Gene Conferring Resistance to Pyrenophora tritici-repentis Race 3 in Tetraploid Wheat. Phytopathology, 96(8), 885-9. doi: 10.1094/PHYTO-96-0885. ID: 18943754.

17.) Kalavacharla V, Hossain K, Gu Y, Riera-Lizarazu O, Vales MI, Bhamidimarri S, Gonzalez-Hernandez JL, Maan SS, Kianian SF (2006 Jun). High-resolution radiation hybrid map of wheat chromosome 1D. Genetics, 173(2), 1089-99. . ID: 16624903.

18.) Conley EJ, Nduati V, Gonzalez-Hernandez JL, Mesfin A, Trudeau-Spanjers M, Chao S, Lazo GR, Hummel DD, Anderson OD, Qi LL, Gill BS, Echalier B, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorák J, Peng JH, Lapitan NL, Pathan MS, Nguyen HT, Ma XF, Miftahudin, Gustafson JP, Greene RA, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sidhu D, Dilbirligi M, Gill KS, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Anderson JA (2004 Oct). A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics, 168(2), 625-37. . ID: 15514040.

19.) Munkvold JD, Greene RA, Bermudez-Kandianis CE, La Rota CM, Edwards H, Sorrells SF, Dake T, Benscher D, Kantety R, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorák J, Miftahudin, Gustafson JP, Pathan MS, Nguyen HT, Matthews DE, Chao S, Lazo GR, Hummel DD, Anderson OD, Anderson JA, Gonzalez-Hernandez JL, Peng JH, Lapitan N, Qi LL, Echalier B, Gill BS, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Erayman M, Gill KS, McGuire PE, Qualset CO, Sorrells ME (2004 Oct). Group 3 chromosome bin maps of wheat and their relationship to rice chromosome 1. Genetics, 168(2), 639-50. . ID: 15514041.

20.) Hossain KG, Kalavacharla V, Lazo GR, Hegstad J, Wentz MJ, Kianian PM, Simons K, Gehlhar S, Rust JL, Syamala RR, Obeori K, Bhamidimarri S, Karunadharma P, Chao S, Anderson OD, Qi LL, Echalier B, Gill BS, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Akhunov ED, Dvorák J, Miftahudin, Ross K, Gustafson JP, Radhawa HS, Dilbirligi M, Gill KS, Peng JH, Lapitan NL, Greene RA, Bermudez-Kandianis CE, Sorrells ME, Feril O, Pathan MS, Nguyen HT, Gonzalez-Hernandez JL, Conley EJ, Anderson JA, Choi DW, Fenton D, (2004 Oct). A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7. Genetics, 168(2), 687-99. . ID: 15514045.

21.) Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorák J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NL, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi D (2004 Oct). A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics, 168(2), 701-12. . ID: 15514046.

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Associations

COBRE

Centers of Biomedical Research Excellence

EPSCoR

Established Program to Stimulate Competitive Research

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Metadata

Links

All the links listed resolve to this core profile

https://www.coremarketplace.org/?FacilityID=1825
https://www.coremarketplace.org/RRID:SCR_023959

Institution

Institution ROR ID: https://ror.org/015jmes13

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

Keywords:

USEDit, ABRF, custom sequencing services, experimental design, bioinformatics data analysis,

Resource Type:

service resource, access service resource, core facility

Citation:

South Dakota State University Genomics Sequencing Core Facility (RRID:SCR_023959)

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Other Facilities at South Dakota State University

SDSU-Functional Genomics Core FacilityRRID:SCR_023786

Services:

Biolayer Interferometry (BLI)

CDNA Synthesis

Cell Imaging

Image Aquisition

Image Processing And Analysis

Real-time qPCR

Widefield Microscopy

Resources:

Contact Info:

1390 College Ave

Rm 047

Brookings, SD 57007 - United States

https://www.sdstate.edu/biology-and-microbiology/functional-genomics-core-facility

Google Maps Location

RRID:

RRID:SCR_023786

Description:

The mission of the FGCF is to provide access and training on a range of instruments in the areas of genomics, molecular biology, imaging, and chemical/metabolite analysis to support research on the SDSU campus.

This facility provides services outside its institution

This facility provides consulting outside its institution

Last updated:

08/02/2023

SDState-Genomics Sequencing Facility (Genomics / Genome Analysis and Technologies)

Quicklinks:

Primary Contact:

Facility RRID

Facility Details

Facility Policies

(To see more facility information, click the in the upper right)

Services offered:

Facility Equipment

(To see more facility information, click the in the upper right)

Publications

(To see more facility information, click the in the upper right)

Associations

COBRE

EPSCoR

(To see more facility information, click the in the upper right)

Metadata

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

Facility Profile QR Code (links to this profile)

(To see more facility information, click the in the upper right)

Filter Results. Click/Unclick items to select.

(To see more facility information, click the in the upper right)

Other Facilities at South Dakota State University

SDSU-Functional Genomics Core FacilityRRID:SCR_023786

(To see more facility information, click the in the upper right)

Contact Jose Gonzalez

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SDState-Genomics Sequencing Facility

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