{"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-15479"],"description":["scATAC-seq of first and second trimester human reproductive tract (including female and male internal and external genitalia)"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Library preparation was carried out according to the manufacturer’s protocol.","Sequencing - Libraries for scATAC-seq were sequenced on Illumina NovaSeq 6000, aiming at a minimum coverage of 10,000 fragments per cell, with the following sequencing format; read 1: 50 cycles; i7 index: 8 cycles, i5 index: 16 cycles; read 2: 50 cycles.","Sample Collection - Single-nuclei suspensions were isolated from dissociated cells when performing scATAC-seq, following the manufacturers’ instructions, and from frozen tissue sections when performing multiomic snRNA-seq/scATAC-seq. For the latter, thick (300 µm) sections were cryosectioned, and kept in a tube on dry ice until subsequent processing. Nuclei were released via Dounce homogenisation as described in detail in the protocols.io.","Nucleic Acid Extraction - For the scATAC-seq and multimodal snRNA-seq/scATAC-seq experiments, cells were loaded according to the manufacturer’s protocol for the Chromium Single Cell ATAC v2  and Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (10X Genomics) to attain between 2,000 and 10,000 cells per well."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - scATAC-seq libraries were processed (read filtering, alignment, barcode counting, and cell calling) with 10x Genomics Cell Ranger ATAC pipeline v.2 using the pre-built 10x GRCh38 genome (version 3.1.0) as reference."],"omics_type":["Unknown","Transcriptomics","Genomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["scATAC-seq"],"species":["Homo sapiens"],"pubmed_authors":["Roser Vento Tormo","Valentina Lorenzi","Luz Garcia Alonso"],"additional_accession":[]},"is_claimable":false,"name":"scATAC-seq of first and second trimester human reproductive tract","description":"scATAC-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":"2025-08-07T23:45:50.117Z","creation":"2025-08-07T23:45:50.117Z"},"accession":"E-MTAB-15479","cross_references":{"ENA":["ERP178531"],"EFO":["EFO_0002944","EFO_0004170","EFO_0010891","EFO_0005518","EFO_0003816","EFO_0004184"]}}