Single-cell Transcriptomic Profiling of Eutopic and Ectopic Endometrial Tissues Across the Menstrual Cycle

Raw and processed feature-barcode matrices are provided for all eutopic and ectopic samples, and split into menstrual cycle phases: proliferative, ovulation, mid-secretory, and late-secretory. Human endometrial tissue was lysed and the cell concentration is adjusted to 700-1200 cells/μL. Gel beads containing the barcode information are combined with the mixture of cells and enzymes, and then encapsulated by oil droplets on the surface of the microfluidic "double cross" system, forming Gel Beads-In-Emulsions (GEMs). GEMs flow into the reservior and are collected, the gel beads dissolve, and the lysed cells release mRNA, which binds to the barcode, UMI, and oligo (dT) sequences on the gel microspheres, reverse transcribing to form cDNA fragments, and labeling the samples. The oil droplets are broken, and PCR amplification is performed using cDNA as the template. The products of all GEMs are mixed to construct a standard seqeucning library. The cDNA is enzymatically digested into fragments of about 200-300 bp, and traditional second-generation sequencing library construction processes such as adding sequencing adapters and primers are performed, followed by PCR amplification to obtain the cDNA library. High-throughput sequencing of the constructed library is performed using the paired-end sequencing mode of the Illumina sequencing platform. 10x Genomics Cell Ranger v. 4.0 (https://support.10xGenomics.com/single-cell-gene-expression/software/overview/welcome) was used to filter, align, quantify, and identify the recovered cells from the raw data, ultimately obtaining the gene expression matrix for each cell. Reads were aligned to the GRCh37 (hg19) reference genome.