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. 2023 Feb 25;60(6):3239–3260. doi: 10.1007/s12035-023-03253-7

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© The Author(s) 2023

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/.

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Fig. 5 — Depletion of circFAT3 leads to loss of neuronal progenitor- and mature cortical neuron-populations in day 90 telencephalic cerebral organoids (COs). A UMAP plot of scRNA-seq data of CTRL and circFAT3 KD-derived cells of day 90 COs (n = 2) clustering of in total of 2714 and 739 cells (cells with > 500 UMI), respectively. Combining both conditions resulted in the identification of 13 clusters in total. NPCs, neural progenitor cells; RGCs, radial glial cells; IPs, intermediate progenitor cells; CPs, choroid plexus cells, CNs, cortical neurons; MSCs, mesenchymal cells, P, progenitors. B Heatmap of selected genes (depicted as mean z-score across cells within a cluster) characterizing the 13 clusters identified in panel A. C UMAP plot of scRNA-seq data from CTRL and circFAT3 KD-derived cells of day 90 COs demonstrating cell origin from either CTRL or circFAT3 KD condition in biological duplicates. Cell position corresponds to cells in panel A. D Quantification of cell numbers per cluster derived from either CTRL or circFAT3 KD day 90 COs. Clusters defined as indicated in A. E Log-normalized expression of selected marker genes from A to B, showing per-cluster specificity and abundance per cell for each gene. F IHC images of day 90 CTRL and circFAT3-depleted COs. MAP2 = magenta; SOX2 = green; DAPI = blue. 12 µm cryostat sections; scale bar = 300 µm. G Quantification of MAP2 signals in day 90 CTRL and circFAT3 COs. The signal intensity was normalized to the area analyzed (µm²). Values are presented as mean ± SEM. N = 6 (CTRL) and n = 7 (circFAT3) from two CO batches. Two-tailed unpaired t-test, *p < 0.05. H IHC images of day 90 CTRL and circFAT3 COs. TUJ1 = magenta; GFAP = green; DAPI = blue. 12 µm cryostat sections; scale bar = 300 µm. I, J Quantification of GFAP (I) and TUJ1 (J) signals in day 90 CTRL and circFAT3 COs. The signal intensity was normalized to the area analyzed (µm²). Values are presented as mean ± SEM. N = 6 (CTRL) and n = 7 (circFAT3) from two CO batches. Two-tailed unpaired t-test, *p < 0.05, ns: not significant