South Dakota State University
Jose Gonzalez
2380 Research Parkway
Brookings, SD 57006
https://www.sdstate.edu/genomics-sequencing-facility
RRID: RRID:SCR_023959
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 × 300 bp read lengths. [Product Link]
RRID:SCR_020134
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
Oxford Nanopore Promethion P2 Solo
Long reads sequencer
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
1.) 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.
2.) 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.
3.) 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.
4.) 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.
5.) 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.
6.) 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.
7.) 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.
8.) 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.
9.) 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.
10.) 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.
11.) 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.
12.) 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.
13.) 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.
14.) 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.
15.) 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.
16.) 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.
17.) 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.
18.) 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.
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.
