title: spatial transcriptomics (10x Visium) of first and second trimester human reproductive tract
library_construction_protocol: Human embryonic and fetal material was provided by the Joint MRC / Wellcome Trust (grant# MR/R006237/1 and MR/X008304/1) Human Developmental Biology Resource (HDBR, http:// www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822 and 23-LO/0312) and Newcastle & North Tyneside 1 Research Ethics Committee (REC reference 18/NE/0290). Fetal reproductive tissue was embedded in OCT and frozen on an isopentane-dry ice slurry.  10x Genomics Visium Spatial Gene Expression protocol was applied to fresh frozen OCT embedded samples. Tissues were sectioned at 10um onto Visium gene expression slides using a Leica CM1950 cryostat. The manufacturer's protocol was followed and H&E stained images of the Visium slides were captured on a Hamamatsu NanoZoomer 2.0HT before permeabilization (optimised at 24-30 mins), reverse transcription and cDNA synthesis using a template-switching protocol, to yield second-strand cDNA from the slide.  10x Genomics Visium CytAssist protocol was applied to fresh frozen OCT embedded samples. Briefly, sections were methanol fixed, H&E stained and imaged on a Hamamatsu Nanozoomer 2.0HT. After destaining, human whole transcriptome probe pairs were hybridised and ligated to the tissue RNA. The ligation products were then released and captured onto Visium slides, using a CytAssist instrument. The probes were then extended to incorporate the spatial barcodes from the Visium slide, eluted and prepared into a dual-indexed library. cDNA from 10x Genomics Visium spatial gene expression slides were prepared into single-indexed libraries using a 10x Genomics PCR-based protocol.   cDNA probes from 10x Genomics Visium CytAssist slides were prepared into dual-indexed libraries using a 10x Genomics PCR-based protocol.  