Creating a high-resolution atlas that depicts the development of the human retina ETH_en NatureBiotech
. In brief, 1 ml of pre-warmed papain solution was added to the organoids and incubated for 10 min at 37 °C. To facilitate dissociation, the mix was pipette-mixed every 5 min with a p1000. Enzyme mix A was added and mixed by inversion and incubated for 10 min at 37 °C. Samples were pipette-mixed until tissue dissociation was confirmed via visual inspection. After incubation, cells were centrifuged for 5 min at 300and 4 °C. Cells were resuspended in 250 μl of PBS + 0.
To integrate single-cell data across timepoints, we merged the scRNA-seq data and multiome data, together with a public scRNA-seq data of retinal organoids. Focusing on the transcriptomic profiles, highly variable genes were identified for each of the three datasets, and those identified in at least two datasets were considered as the overall highly variable genes. Data scaling and PCA were performed, and sample integration was performed using CSSstratified on samples .
Cells of all the scATAC-seq data, as well as those of the multiome data, were merged and integrated, considering their accessibility profiles across the unified peak list, using CSS stratified on samples, after data normalization with TFIDF and generating LSI representation with SVD using peaks detected in more than 0.5% of cells. PCA was performed on the resulting CSS matrix to get the PCA-reduced CSS representation .
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