{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Valentina Lorenzi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15471"],"description":["spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Unknown","Transcriptomics","Genomics"],"instrument_platform":["Illumina HiSeq 4000"],"study_type":["spatial transcriptomics by high-throughput sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Roser Vento Tormo","Valentina Lorenzi","Luz Garcia Alonso"],"additional_accession":[]},"is_claimable":false,"name":"spatial transcriptomics (10x Visium) of first and second trimester human reproductive tract","description":"spatial transcriptomics by means of 10x Visium of first and second trimester human reproductive tract (including female and male internal and external genitalia)","dates":{"release":"2025-08-06T00:00:00Z","modification":"2025-08-06T13:49:44.53Z","creation":"2025-08-06T13:49:44.53Z"},"accession":"E-MTAB-15471","cross_references":{"ENA":["ERP177889"],"EFO":["EFO_0002944","EFO_0004170","EFO_0030005","EFO_0005518","EFO_0003816","EFO_0004184"]}}