A single-cell transcriptomic analysis of endometriosis

We profiled transcriptomes of >370,000 individual cells from endometriomas (n=8), endometriosis (n=28), eutopic endometrium (n=10), unaffected ovary (n=4) and endometriosis-free peritoneum (n=4) to create a cellular atlas of endometrial-type epithelial cells, stromal cells, and microenvironmental cell populations across tissue sites. Overall design: Single cells are captured and barcoded using the 10X Chromium platform (10X Genomics). scRNA-seq libraries were prepared following the instructions from Chromium Single Cell 3' Reagent Kits User Guide (v2 or v3). Briefly, Gel Bead-In EMulsions (GEMs) are generated using single cell preparations. After GEM-RT and cleanup, the cDNA from barcoded single cell RNAs were amplified before quantification using Agilent Bioanalyzer High Sensitivity DNA chips. The single cell 3' gene expression libraries were constructed and cDNA corresponding to an insertion size of around 350 bp selected. Libraries were quantified using Agilent Bioanalyzer High Sensitivity DNA chips and pooled together to get similar numbers of reads from each single cell before sequencing on the NovaSeq S4 (by Fulgent Genomics or Novogene).