Van Andel Institute

Contact Info:

VAI Spatial Services

333 Bostwick Ave NE

Grand Rapids, MI 49503

https://genomicscore.vai.org

Grants and Identifiers:

RRID: RRID:SCR_022913

Instrumentation:

Services Provided:

10x Genomics

10x Genomics Visium

10x Genomics Xenium Spatial Transcriptomics

Bisulfite Conversion

ChIP-Seq

CITE-seq

Consultations

CUT&RUN

CUT&Tag

Digital PCR

FFPE Restore

Genomics

Methylation Analysis

Microarray

Nanopore Sequencing

NanoString GeoMx DSP

Reduced Representation Bisulfite Sequencing

Ribosomal Reduction

RNA Integrity

RNAseq

Sample Preparation

Sequencing - Next Generation Sequencing (NGS)

Single-cell Sequencing

Spatial Transcriptomics

Visium HD Spatial Transcriptomics

Whole Exome Sequencing

Whole Genome Sequencing

Relevant Publications:

1.) Zhong ZA, Michalski MN, Diegel CR, Christie C, Klamer Z, Lanning NJ, Haab BB, Grainger S, Williams BO (2025 Dec 17). Local Misalignment Scoring Reveals Spatially Uniform Chondrocyte Disorganization in a Wnt5a-C83S Knock-in Model of Robinow Syndrome. Research square, (), . . PMCID: 12776500.

2.) Oswald BM, DeCamp LM, Longo J, Dahabieh MS, Bunda N, Johnson BK, Watson MJ, Ma S, Preston SE, Sheldon RD, Vincent MP, Ellis AE, Soper-Hopper MT, Isaguirre C, Kamarudin D, Shen H, Williams KS, Crawford PA, Kaech S, Jang HJ, Lien EC, Krawczyk CM, Jones RG (2025 Dec 9). Dietary restriction reprograms CD8+ T cell fate to enhance anti-tumour immunity and immunotherapy responses Nature Metabolism, 7(12), 2489-2509. . PMCID: 12727518.

3.) Diegel CR, Michalski MN, Ubels JL, Wiartalla GF, Lin CM, Zhong ZA, McDonald MJ, Ethen NJ, Brookshire M, Madaj ZB, Xia M, Gavine PR, Antonetti DA, Williams BO (2025 Nov 11). The class A repeats of LRP5 are required for normal development of bone, retinal vasculature and mammary gland in vivo Disease Models & Mechanisms, 18(11), dmm052280. . PMCID: 12661645.

4.) Finneran DJ, Jackman BM, Desjarlais T, Henry A, Soliman AS, Muskus PC, Shankar R, Chen B, Nash KR, Morgan D, Gordon MN (2025 Nov 5). Mature tau pathology is not improved by interfering with interleukin-1 receptor signaling in two mouse models of tauopathy PLOS One, 20(11), e0335409. . PMCID: 12588532.

5.) Chomiak AA, Wiseman AK, Hrit J, Liu Y, Stransky S, Sidoli S, Tiedemann RL, Rothbart SB (2025 Sep 18). Dual EZH1/2 inhibition enhances DNMT inhibitor efficacy in colon cancer through targeting H3K27me1 bioRxiv, (), 2025.09.16.676613. . PMCID: 12458120.

6.) Liu Y, Zhao Y, Liu M, Kim P, Liao J, Lu D, Liu H, Szabó PE, Yang T (2025 Sep 8). EHMT2 Controls Neural Crest-Derived Craniofacial Development but is Dispensable in Limb Development bioRxiv, (), 2025.09.07.674526. . PMCID: 12439983.

7.) Longo J, DeCamp LM, Oswald BM, Teis R, Reyes-Oliveras A, Dahabieh MS, Ellis AE, Vincent MP, Damico H, Gallik KL, Foy NM, Compton SE, Capan CD, Williams KS, Esquibel CR, Madaj ZB, Lee H, Roy DG, Krawczyk CM, Haab BB, Sheldon RD, Jones RG (2025 Sep 2). Glucose-dependent glycosphingolipid biosynthesis fuels CD8(+) T cell function and tumor control. Cell metabolism, 37(9), 1890-1906.e11. . PMID: 40769148.

8.) Pérez-Mojica JE, Madaj ZB, Isaguirre C, Roy J, Lau KH, Sheldon RD, Lempradl A (2025 Aug 13). Resolving early embryonic metabolism in Drosophila through single-embryo metabolomics and transcriptomics Nature Metabolism, 7(10), 2165-2177. . PMCID: 12552126.

9.) Spix NJ, Habib WA, Zhang Z, Eugster E, Milliron HY, Sokol D, Lee K, Nolte PA, Endicott JL, Krzyzanowski KF, Hinoue T, Morrison J, Johnson BK, Zhou W, Shen H, Laird PW (2025 Jul 8). High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics Nature Communications, 16(), 6273. . PMCID: 12234882.

10.) Jones P, Liu M, Urrutia G, Shereda R, Thomas S, Liang G (2025 Jul 1). Dnmt3a2 expression during embryonic development is required for phenotypic stability Research Square, (), rs.3.rs-6908216. . PMCID: 12236915.

11.) Dahabieh MS, DeCamp LM, Oswald BM, Kitchen-Goosen SM, Fu Z, Vos M, Compton SE, Longo J, Foy NM, Williams KS, Ellis AE, Johnson A, Sodiya I, Vincent M, Lee H, Yao C, Wu T, Sheldon RD, Krawczyk CM, Jones RG (2025 Jun 27). The prostacyclin receptor PTGIR is a NRF2-dependent regulator of CD8+ T cell exhaustion Nature Immunology, 26(7), 1139-1151. . PMCID: 12208871.

12.) Grimes B, DenHaan K, Becker K, Adams M (2025 Jun 16). Comparing Novel Low-Input Total RNA-Seq Methods Journal of Biomolecular Techniques : JBT, 36(3), 3fc1f5fe.9a29c7c5. . PMCID: 12707489.

13.) Beddows I, Djirackor S, Omran DK, Jung E, Shih NN, Roy R, Hechmer A, Olshen A, Adelmant G, Tom A, Morrison J, Adams M, Rohrer DC, Schwartz LE, Pearce CL, Auman H, Marto JA, Drescher CW, Drapkin R, Shen H (2025 Mar 26). Impact of BRCA mutations, age, surgical indication, and hormone status on the molecular phenotype of the human Fallopian tube Nature Communications, 16(), 2981. . PMCID: 11947093.

14.) Xue Z, Xuan H, Lau K, Su Y, Wegener M, Li K, Turner L, Adams M, Shi X, Wen H (2025 Mar 14). Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney development Nature Communications, 16(), 2531. . PMCID: 11909213.

15.) Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Yang CH, Bergsma A, Drougard A, Dror E, Chandler DP, Schramek D, Triche TJ Jr, Pospisilik JA (2025 Jan 24). TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states Nature Cancer, 6(2), 385-403. . PMCID: 11864977.

16.) Liu Y, Hrit JA, Chomiak AA, Stransky S, Hoffman JR, Tiedemann RL, Wiseman AK, Kariapper LS, Dickson BM, Worden EJ, Fry CJ, Sidoli S, Rothbart SB (2025 Jan 16). DNA hypomethylation promotes UHRF1-and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states. Molecular cell, 85(2), 394-412.e12. . PMID: 39631394.

17.) Pierce SE, van der Schans EJC, Goralski TM, Ensink E, Li P, Henderson MX, Coetzee GA (2025). Gene expression asymmetry in Parkinson's disease: variation of CCT gene expression is correlated with hemisphere specific severity. Frontiers in molecular neuroscience, 18(), 1743557. . PMCID: 12835222.

18.) Liu (刘延晴) Y, Hrit JA, Chomiak AA, Stransky S, Hoffman JR, Tiedemann RL, Wiseman AK, Kariapper LS, Dickson BM, Worden EJ, Fry CJ, Sidoli S, Rothbart SB (2024 Dec 3). DNA hypomethylation promotes UHRF1- and SUV39H1/H2-dependent crosstalk between H3K18ub and H3K9me3 to reinforce heterochromatin states Molecular cell, 85(2), 394-412.e12. . PMCID: 11741932.

19.) Jang HJ, Urrutia G, Orskov AD, Kim HJ, Nelson SA, Nguyen AV, Lee H, Burgos RS, Johnson BK, Wegener M, Becker K, Adams M, Sheridan R, Ramjan ZH, Givan SA, Zebley CC, Youngblood BA, Issa JJ, Topper MJ, Baylin SB, Baer MR, Triche TJ, O'Connell CL, Gronbaek K, Jones PA (2024 Nov 11). Bone marrow microenvironment signatures associate with patient survival after guadecitabine and atezolizumab therapy in HMA-resistant MDS. bioRxiv : the preprint server for biology, (), . . PMID: 39605731.

20.) Vatsa N, Brynildsen JK, Goralski TM, Kurgat K, Meyerdirk L, Breton L, DeWeerd D, Brasseur L, Turner L, Becker K, Gallik KL, Bassett DS, Henderson MX (2024 Oct 22). Network analysis of α-synuclein pathology progression reveals p21-activated kinases as regulators of vulnerability bioRxiv, (), 2024.10.22.619411. . PMCID: 11526907.

21.) Xue Z, Qin L, Xuan H, Luo K, Huang M, Xie L, Su Y, Xu L, Harsh J, Dale B, Shi X, Chen X, Kaniskan HÜ, Jin J, Wen H (2024 Aug 28). A potent and selective ENL degrader suppresses oncogenic gene expression and leukemia progression Science Advances, 10(35), eado1432. . PMCID: 11352836.

22.) Guak H, Weiland M, Ark AV, Zhai L, Lau K, Corrado M, Davidson P, Asiedu E, Mabvakure B, Compton S, DeCamp L, Scullion CA, Jones RG, Nowinski SM, Krawczyk CM (2024 Jul 24). Transcriptional programming mediated by the histone demethylase KDM5C regulates dendritic cell population heterogeneity and function Cell reports, 43(8), 114506. . PMCID: 11416765.

23.) Kochmanski J, Virani M, Kuhn NC, Boyd SL, Becker K, Adams M, Bernstein AI (2024 Apr 29). Developmental origins of Parkinson’s disease risk: perinatal exposure to the organochlorine pesticide dieldrin leads to sex-specific DNA modifications in critical neurodevelopmental pathways in the mouse midbrain bioRxiv, (), 2024.04.26.590998. . PMCID: 11092502.

24.) Chomiak AA, Tiedemann RL, Liu Y, Kong X, Cui Y, Wiseman AK, Thurlow KE, Cornett EM, Topper MJ, Baylin SB, Rothbart SB (2024 Mar 27). Select EZH2 inhibitors enhance viral mimicry effects of DNMT inhibition through a mechanism involving NFAT:AP-1 signaling Science Advances, 10(13), eadk4423. . PMCID: 10971413.

25.) Goralski TM, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse DJ, Henderson MX (2024 Mar 26). Spatial transcriptomics reveals molecular dysfunction associated with cortical Lewy pathology Nature Communications, 15(), 2642. . PMCID: 10966039.

26.) Tiedemann RL, Hrit J, Du Q, Wiseman AK, Eden HE, Dickson BM, Kong X, Chomiak AA, Vaughan RM, Hebert JM, David Y, Zhou W, Baylin SB, Jones PA, Clark SJ, Rothbart SB (2024 Feb 16). UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation. bioRxiv : the preprint server for biology, (), . . PMID: 38405904.

27.) Booms A, Pierce SE, van der Schans EJ, Coetzee GA (2024 Jan 17). Parkinson’s disease risk enhancers in microglia iScience, 27(2), 108921. . PMCID: 10845915.

28.) Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, Chandler D, Schramek D, Triche TJ Jr, Pospisilik JA (2023 Sep 15). Developmental priming of cancer susceptibility bioRxiv, (), 2023.09.12.557446. . PMCID: 10515831.

29.) Pérez-Mojica JE, Enders L, Lau KH, Lempradl A (2023 Sep 7). Single-embryo RNA sequencing for continuous and sex-specific gene expression analysis on Drosophila STAR Protocols, 4(3), 102535. . PMCID: 10493594.

30.) Paul EN, Carpenter TJ, Fitch S, Sheridan R, Lau KH, Arora R, Teixeira JM (2023 Jul 3). Cysteine-rich intestinal protein 1 is a novel surface marker for human myometrial stem/progenitor cells Communications Biology, 6(), 686. . PMCID: 10317972.

31.) Goralski T, Meyerdirk L, Breton L, Brasseur L, Kurgat K, DeWeerd D, Turner L, Becker K, Adams M, Newhouse D, Henderson MX (2023 May 17). Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology bioRxiv, (), 2023.05.17.541144. . PMCID: 10245657.

32.) Paul EN, Carpenter TJ, Fitch S, Sheridan R, Lau KH, Arora R, Teixeira JM (2023 Mar 18). Cysteine-Rich Intestinal Protein 1 is a Novel Surface Marker for Myometrial Stem/Progenitor Cells bioRxiv, (), 2023.02.20.529273. . PMCID: 10054937.

Description:

Full service Next Generation Sequencing, Single Cell Genomics, and Spatial Transcriptomics facility. Provides the services in: - experimental design support - NGS library generation - Illumina, Element and Nanopore Sequencing - single cell preparation and library generation - spatial slide preparation and imaging - spatial transcriptomic and epigenomic profiling