Abstract
Spatial transcriptomics allows for the genome-wide profiling of topographic gene expression patterns within a tissue of interest. Here, we describe our methodology to generate high-quality RNA-seq libraries from cryosections from fresh frozen mouse whole olfactory mucosae. This methodology can be extended to virtually any vertebrate organ or tissue sample.
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References
Kurian SM, Naressi RG, Manoel D, Barwich AS, Malnic B, Saraiva LR (2021) Odor coding in the mammalian olfactory epithelium. Cell Tissue Res 383:445–456
Ressler KJ, Sullivan SL, Buck LB (1993) A zonal organization of odorant receptor gene expression in the olfactory epithelium. Cell 73(3):597–609
Vassar R, Ngai J, Axel R (1993) Spatial segregation of odorant receptor expression in the mammalian olfactory epithelium. Cell 74(2):309–318
Strotmann J, Wanner I, Krieger J, Raming K, Breer H (1992) Expression of odorant receptors in spatially restricted subsets of chemosensory neurones. Neuroreport 3:1053–1056
Miyamichi K, Serizawa S, Kimura HM, Sakano H (2005) Continuous and overlapping expression domains of odorant receptor genes in the olfactory epithelium determine the dorsal/ventral positioning of glomeruli in the olfactory bulb. J Neurosci 25:3586–3592
Zapiec B, Mombaerts P (2020) The zonal organization of odorant receptor gene choice in the main olfactory epithelium of the mouse. Cell Rep 30(12):4220–4234 e5
Saraiva LR, Riveros-McKay F, Mezzavilla M, Abou-Moussa EH, Arayata CJ, Makhlouf M, Trimmer C, Ibarra-Soria X, Khan M, Van Gerven L et al (2019) A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans. Sci Adv 5:eaax0396
Ibarra-Soria X, Nakahara TS, Lilue J, Jiang Y, Trimmer C, Souza MA, Netto PH, Ikegami K, Murphy NR, Kusma M et al (2017) Variation in olfactory neuron repertoires is genetically controlled and environmentally modulated. elife 6
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW (2015) Molecular and neuronal homology between the olfactory systems of zebrafish and mouse. Sci Rep 5:11487
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW (2015) Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq. Sci Rep 5:18178
Horowitz LF, Saraiva LR, Kuang D, Yoon KH, Buck LB (2014) Olfactory receptor patterning in a higher primate. J Neurosci 34:12241–12252
Ibarra-Soria X, Levitin MO, Saraiva LR, Logan DW (2014) The olfactory transcriptomes of mice. PLoS Genet 10:e1004593
Asp M, Bergenstrahle J, Lundeberg J (2020) Spatially resolved transcriptomes-next generation tools for tissue exploration. Bioessays 42(10):e1900221
Junker JP, Noel ES, Guryev V, Peterson KA, Shah G, Huisken J, McMahon AP, Berezikov E, Bakkers J, van Oudenaarden A (2014) Genome-wide RNA Tomography in the zebrafish embryo. Cell 159:662–675
Ruiz Tejada Segura ML, Abou Moussa E, Garabello E, Nakahara TS, Makhlouf M, Mathew LS, Wang L, Valle F, Huang SSY, Mainland JD et al (2022) A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell. Cell Rep 38:110547
Acknowledgments
We want to thank the Integrated Genomic Services of Sidra Medicine for the technical support. This work was supported by Sidra Medicine (grant SDR400040 to L.R.S.) – a member of Qatar Foundation.
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Moussa, E.A., Makhlouf, M., Mathew, L.S., Saraiva, L.R. (2023). Genome-Wide RNA Tomography in the Mouse Whole Olfactory Mucosa. In: Goldstein, B.J., Matsunami, H. (eds) The Olfactory System. Methods in Molecular Biology, vol 2710. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3425-7_2
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DOI: https://doi.org/10.1007/978-1-0716-3425-7_2
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