{"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-15475"],"description":["scRNA-seq of first and second trimester human reproductive tract (including female and male internal and external genitalia)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - For the scRNA-seq experiments, cells were loaded according to the manufacturer’s protocol for the Chromium Next GEM Single Cell 5′ v2 (DUAL) Kit  (10X Genomics) to attain between 2,000 and 10,000 cells per reaction.","Library Construction - Library preparation was carried out according to the manufacturer’s protocol.","Sample Collection - We used the previous protocol optimised for gonadal dissociation and available at protocols.io136. In short, tissues were cut into <1 mm3 segments before being digested with a mix of Trypsin-EDTA 0.25% and DNaseI (0.1mg/ml) for 5-15 minutes at 37°C with intermittent shaking. Samples > 17 PCW were digested using a combination of collagenase and Trypsin/EDTA, a protocol adapted from Wagner et al.,136,137. In short, samples were first digested with a mix of Collagenase 1A (1 mg/ml), DNaseI (0.1 mg/ml) and Liberase TM (50 µg/ml) for 45 minutes at 37°C with rotation. Cell solution was further digested with Trypsin/EDTA 0.25% for 10 minutes at 37°C with rotation. In both protocols, digested tissue was passed through a 100 µm filter, and cells collected by centrifugation (500 x g for 5 minutes at 4°C). Cells were washed and resuspended in PBS-BSA 0.04% prior to cell counting.","Sequencing - Libraries were sequenced, aiming at a minimum coverage of 20,000 raw reads per cell, on the Illumina HiSeq 4000 or Novaseq 6000 systems; using the sequencing format; read 1: 26 cycles; i7 index: 8 cycles, i5 index: 0 cycles; read 2: 98 cycles."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - For each sequenced scRNA-seq library, we performed read alignment to the human reference genome (GRCh38 2020-A), mRNA quantification and initial quality control using STARsolo141 with default parameters."],"omics_type":["Unknown","Transcriptomics","Genomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Roser Vento Tormo","Valentina Lorenzi","Luz Garcia Alonso"],"additional_accession":[]},"is_claimable":false,"name":"scRNA-seq of first and second trimester human reproductive tract","description":"scRNA-seq of first and second trimester human reproductive tract (including female and male internal and external genitalia)","dates":{"release":"2025-08-07T00:00:00Z","modification":"2025-08-07T13:35:33.536Z","creation":"2025-08-07T13:35:33.536Z"},"accession":"E-MTAB-15475","cross_references":{"ENA":["ERP178525"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}