Comparative Eye Transcriptome Atlas

The Comparative Eye Transcriptome Atlas provides transcriptomic resources to study retinal evolution and physiology across non-mammalian vertebrates. We profiled retinas from four species using two complementary high-throughput approaches. Eight 10x Genomics Visium spatial transcriptomics datasets were generated from Anolis carolinensis (n = 2), Taeniopygia guttata (n = 4), Columba livia (n = 1), and Gallus gallus (n = 1), capturing spatially resolved gene expression with matched histology images. In parallel, six 10x Genomics Chromium Single Cell 3' RNA-seq datasets were obtained from zebra finch (T. guttata) retinas to resolve cell-type–specific transcriptomes. Raw sequencing data (FASTQ) and processed outputs from SpaceRanger (Visium) and CellRanger (Chromium) are provided. Downstream integrated and annotated datasets can be explored interactively at https://linlab.au.dk/Damsgaard_lab/CETA/ and full Seurat objects are available on request. Overall design: Retinas were dissected from healthy adult animals of four species: the green anole (Anolis carolinensis; n = 2), zebra finch (Taeniopygia guttata; n = 4 for Visium, n = 6 for Chromium), rock pigeon (Columba livia; n = 1), and chicken (Gallus gallus; n = 1). For spatial transcriptomics, retinas were cryosectioned and processed with the 10x Genomics Visium Spatial Gene Expression kit v1 (55 µm spot resolution) and imaged at 20× magnification before library preparation. For single-cell transcriptomics, retinas from zebra finches were dissociated and processed with the 10x Genomics Chromium Single Cell 3' v3 workflow. All libraries were sequenced on an Illumina HiSeq 4000 using paired-end 2 × 150 bp reads. Raw data were processed with SpaceRanger 3.1.1 (Visium) and CellRanger 7.1.0 (Chromium) against the following reference genomes: AnoCar3.1 (A. carolinensis), TaeGut1 (T. guttata), Cliv_2.1 (C. livia), and GRCg7b (G. gallus). The processed data deposited here are the standard filtered outputs of these pipelines without additional ambient RNA removal, doublet removal, or downstream QC filtering.