Project description:Domestic rock pigeons (Columba livia) homozygous for either of two “recessive red” mutations, which are partially-overlapping deletions causing downregulation of Sox10, display brilliant red colors instead of blue/black feathers. Sox10 encodes a transcription factor important for melanocyte differentiation and function, but the precise role that it plays in promoting eumelanin over pheomelanin pigment production in pigeons are unknown. In this study, we perform ChIPseq for SOX10, H3K27ac, and H3K27me3 to better understand the genome occupancy of SOX10 in avian melanocytes.
Project description: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.
