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. 2021 Sep 14;22:661. doi: 10.1186/s12864-021-07930-6

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — Downstream analysis of the dr_pineal_s2 dataset. a 2D visualization using UMAP of Cell Ranger analyzed clusters. Each point represents a single cell, colored according to cell type. The cells were clustered into 13 distinct types, which were defined according to their unique transcriptomes (Additional file 2). b Expression profile of marker genes according to cluster [7] of (a). Cone- and rod-like PhRs are defined according to their transducin protein subunits (gnat1 and gngt1 in rods vs. gnat2 and gngt2a in cones [25]), as well as their unique opsins (exorh in rod-like [26] and opn1lw1 and parietopsin in cone-like). c 2D visualization using UMAP of kallisto analyzed clusters. Each point represents a single cell, colored according to cell type. The cells were clustered into 14 distinct types, which were defined according to their unique transcriptomes (Additional file 2). d Expression profile of marker genes according to cluster [7] of (c). Two different populations of cone-like PhRs are detected. Both express the cone unique transducin protein-subunits, but differ in the expressed opsin (opn1lw1 in red-cones, and parietopsin in green-cones), demonstrating the bi-chromatic photoreception characteristic of the pineal gland. col14a1b was only detected in the kallisto dataset and is the strongest DE marker within the red-cone cluster (c, d)