Single-cell Multi-omics Atlas of Somites from Normal and Growth-Retarded Duroc x Tibetan Pig Embryos at E21

Preparation of single cell water-in-oil droplets according to 10×Genomics Single Cell 3' Reagent Kits v2 Guide. Droplets were reverse transcribed and amplified by Veriti 96-well thermal cycler (Thermo Fisher, USA). cDNA was then purified using SPRIselect magnetic beads (Beckman, USA) and on a bioanalyzer to determine the concentration. According to the Single Cell 3’Reagent Kit v3 user guide to prepare cDNA libraries.The raw data gene expression matrix was processed using R (v.3.5.2).

Dimensionality reduction, clustering, and visualization of scRNA-seq data were conducted using Seurat (v.4.0) with default parameters. ScATAC-seq data were analysed by ArchR. The raw data files are in FASTQ format, while the processed data include features (genes/peaks), cell barcodes, and expression/accessibility count matrices.