biostudies-arrayexpressValentina LorenziHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15471spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)biostudies-arrayexpressSample Collection - 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.Library Construction - 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.Nucleic Acid Extraction - 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.Sequencing - 10x Genomics Visium spatial gene expression libraries were sequenced (1 per lane on a HiSeq4000), aiming for 300M raw reads per sample, with the following sequencing format; read 1: 28 cycles, i7 index: 8 cycles, i5 index: 0 cycles and read 2: 91 cycles. 10x Genomics Visium CytAssist libraries were sequenced (4 samples per Illumina Novaseq SP flow cell) aiming for a minimum 25,000 read pairs per spot, with the sequencing format; read 1: 28 cycles, i7 index: 10 cycles, i5 index: 10 cycles and read 2S: 90 cycles.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Visium data consists of FASTQ sequencing files and a bright-field microscopy image stained with haematoxylin and eosin (H&E) per capture area. The Space Ranger (v2.0.0) software provided by 10x Genomics was employed to align the barcoded spot pattern to the H&E tissue image and to differentiate tissue from background. The resulting spot-by-transcript abundance matrix was analysed using the package squidpy.UnknownTranscriptomicsGenomicsIllumina HiSeq 4000spatial transcriptomics by high-throughput sequencingHomo sapiensRoser Vento TormoValentina LorenziLuz Garcia Alonsofalsespatial transcriptomics (10x Visium) of first and second trimester human reproductive tractspatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)2025-08-06T00:00:00Z2025-08-06T13:49:44.53Z2025-08-06T13:49:44.53ZE-MTAB-15471ERP177889EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184