About
To construct multi-omics atlas of Drosophila development, we first generated 3D spatial transcriptomes throughout development. Developing embryos were collected at 0.5 to 2 h intervals throughout embryogenesis. Larva samples were collected at early or late time points for each of the three larval stages. Pupa samples were collected at 12 h intervals starting from pupation. Cryosection was performed for each sample to obtain their sagittal sections of 7 or 8 μm thickness, and all available sections of each sample were subjected to in situ mRNA capture, library preparation, and sequencing at the Stereo-seq platform. Utilizing Stereo-seq, we generated organism-wide single-cell spatial transcriptomes for 43 embryo, 9 larva, and 5 pupa samples throughout Drosophila development, with a total of 3,812,505 cell bins. We further collected samples at 2-hour intervals across embryogenesis and performed droplet-based scRNA-seq and scATAC-seq. Following quality control, we obtained 238,242 single-cell transcriptomes with scRNA-seq, with a median of 6,841 UMIs and 1,707 genes per cell. Additionally, we obtained 240,573 single-cell chromatin accessibility profiles with scATAC-seq, with a median of 11,772 fragments per cell.
Accessions
CNSA-project: CNP0005060
STOmics DB-Project: STT0000069
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