Rathnakumar Kumaragurubaran
3333 Burnet Avenue
Cincinnati, OH 45229-3026
https://www.cincinnatichildrens.org/research/cores/single-cell-genomics
RRID: RRID:SCR_022653
10X Genomics Chromium Plus Genetic Analyzer
Genetic analyzer, referred to as Chromium Controller for combining large partition numbers with a diverse barcode library to generate >100,000 barcode-containing partitions. [Product Link]
RRID:SCR_019326
1.) Tominaga K, Kechele DO, Sanchez JG, Vales S, Jurickova I, Roman L, Asai A, Enriquez JR, McCauley HA, Kishimoto K, Iwasawa K, Singh A, Horio Y, Múnera JO, Takebe T, Zorn AM, Helmrath MA, Denson LA, Wells JM (2024 Dec 17). Deriving Human Intestinal Organoids with Functional Tissue-Resident Macrophages All From Pluripotent Stem Cells Cellular and Molecular Gastroenterology and Hepatology, 19(4), 101444. . PMCID: 11847122.
2.) He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA (2024 Sep 16). PRDM3/16 regulate chromatin accessibility required for NKX2-1 mediated alveolar epithelial differentiation and function Nature Communications, 15(), 8112. . PMCID: 11405758.
3.) Al Reza H, Santangelo C, Al Reza A, Iwasawa K, Sachiko S, Glaser K, Bondoc A, Merola J, Takebe T (2024 Aug 30). Self-Assembled Generation of Multi-zonal Liver Organoids from Human Pluripotent Stem Cells bioRxiv, (), 2024.08.30.610426. . PMCID: 11384014.
4.) Waggoner S, Cox A, Canaday L, Katko A, Feldman H, Warrick K, Tselikova A, Seelamneni H, Roskin K (2024 Aug 30). KLF2 determines the susceptibility of T cells to immunoregulatory NK cells Research Square, (), rs.3.rs-4921081. . PMCID: 11384801.
5.) Stepanchick E, Wilson A, Sulentic AM, Choi K, Hueneman K, Starczynowski DT, Chlon TM (2024 Jun 27). DDX41 haploinsufficiency causes inefficient hematopoiesis under stress and cooperates with p53 mutations to cause hematologic malignancy Leukemia, 38(8), 1787-1798. . PMCID: 11286521.
6.) Dao L, You Z, Lu L, Xu T, Sarkar AK, Zhu H, Liu M, Calandrelli R, Yoshida G, Lin P, Miao Y, Mierke S, Kalva S, Zhu H, Gu M, Vadivelu S, Zhong S, Huang LF, Guo Z (2024 Jun 6). Modeling blood-brain barrier formation and cerebral cavernous malformations in human PSC-derived organoids. Cell stem cell, 31(6), 818-833.e11. . PMID: 38754427.
7.) Wayman JA, Yang Z, Angerman E, Bonkowski E, Jurickova I, Chen X, Bejjani AT, Parks L, Parameswaran S, Miethke AG, VanDussen KL, Dhaliwal J, Weirauch MT, Kottyan LC, Denson LA, Miraldi ER (2024 Feb 13). Accessible chromatin maps of inflammatory bowel disease intestine nominate cell-type mediators of genetic disease risk. bioRxiv : the preprint server for biology, (), . . PMID: 38405748.
8.) Krishnan JM, Roskin KM, Meeds HL, Blackard JT (2024). Effect of fentanyl on HIV expression in peripheral blood mononuclear cells. Frontiers in microbiology, 15(), 1463441. . PMID: 39386369.
9.) He H, Bell SM, Davis AK, Zhao S, Sridharan A, Na CL, Guo M, Xu Y, Snowball J, Swarr DT, Zacharias WJ, Whitsett JA (2023 Dec 20). PRDM3/16 Regulate Chromatin Accessibility Required for NKX2-1 Mediated Alveolar Epithelial Differentiation and Function bioRxiv, (), 2023.12.20.570481. . PMCID: 10769259.
10.) Múnera JO, Kechele DO, Bouffi C, Qu N, Jing R, Maity P, Enriquez JR, Han L, Campbell I, Mahe MM, McCauley HA, Zhang X, Sundaram N, Hudson JR, Zarsozo-Lacoste A, Pradhan S, Tominaga K, Sanchez JG, Weiss AA, Chatuvedi P, Spence JR, Hachimi M, North T, Daley GQ, Mayhew CN, Hu YC, Takebe T, Helmrath MA, Wells JM (2023 Nov 2). Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon Cell stem cell, 30(11), 1434-1451.e9. . PMCID: 10913028.
11.) Shi T, Burg AR, Caldwell JT, Roskin KM, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso JA, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA (2023 Jul 17). Single-cell transcriptomic analysis of renal allograft rejection reveals insights into intragraft TCR clonality The Journal of Clinical Investigation, 133(14), e170191. . PMCID: 10348771.
12.) Shanmuganad S, Ferguson A, Paranjpe A, Cianciolo EE, Katz JD, Herold MJ, Hildeman DA (2023 Mar 2). Subset-specific and temporal control of effector and memory CD4+ T cell survival. bioRxiv : the preprint server for biology, (), . . PMID: 36909576.
13.) Shi T, Burg AR, Caldwell JT, Roskin K, Castro-Rojas CM, Chukwuma PC, Gray GI, Foote SG, Alonso J, Cuda CM, Allman DA, Rush JS, Regnier CH, Wieczorek G, Alloway RR, Shields AR, Baker BM, Woodle ES, Hildeman DA (2023 Feb 13). Single cell transcriptomic analysis of renal allograft rejection reveals novel insights into intragraft TCR clonality. bioRxiv : the preprint server for biology, (), . . PMID: 36798151.
14.) Khorki ME, Shi T, Cianciolo EE, Burg AR, Chukwuma PC, Picarsic JL, Morrice MK, Woodle ES, Maltzman JS, Ferguson A, Katz JD, Baker BM, Hildeman DA (2023). Prior viral infection primes cross-reactive CD8+ T cells that respond to mouse heart allografts. Frontiers in immunology, 14(), 1287546. . PMID: 38143762.
The Single Cell Genomics Facility (SCGF) offers advanced gene expression and epigenome analysis, capable of simultaneously examining thousands of genes using microfluidics and microwell-based technologies. Additionally, the SCGF provides spatial transcriptomics profiling at both standard (Visium, 55um) and high resolution (Visium HD, 2um) levels, as well as in situ panel-based approaches (10X Xenium)
