{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gaja Matassa"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15528"],"description":["Low-pass whole genome sequencing (WGS) of one sample of human induced pluripotent stem cells (hiPSCs) derived from the CTL08A male cell line and three samples of CTL08A human embryonic germ cell-like cells (hEGCLCs) at passage 10 after hPGCLC-hEGCLC conversion."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - hiPSCs, hEGCLCs were washed in DPBS, detached and dissociated into single-cell using Accutase (Sigma-Aldrich, #A6964). The cell suspension was washed in DPBS and centrifuged at 600g for 5 minutes. The pellet was snap-frozen in dry ice and stored at -80°C.","Library Construction - Library were constructed following Illumina DNA PCR-Free Library Prep Standard Input Workflow (Document #1000000086922 v03)","Nucleic Acid Extraction - Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, #69504),following manufacturer's instructions.","Sequencing - Library were sequenced with Illumina, on NovaSeq6000"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The processed bam files are the results of adapter trimming with fastp, alignment with BWA-MEM (GRCh38.p13), deduplication with MarkDuplicates and removal of chrY reads for the legal constraints of the cell line."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","NovaSeq6000"],"pubmed_abstract":["Primordial germ cells (PGCs) are the embryonic precursors of the gametes. In rodents, PGCs readily form self-renewing embryonic germ cell (EGC) lines in vitro. Although human PGCs undergo a similar conversion during germ cell tumorigenesis, no comparable in vitro system has yet been established in humans. Here we report that hPGC-like cells (hPGCLCs) undergo conversion to human EGC-like cells (hEGCLCs) using the inductive signals previously identified in mice. This feeder-free culture system allows efficient derivation of hEGCLCs that are transcriptionally similar to human induced pluripotent stem cells and can give rise to hPGCLCs once more demonstrating the interconvertibility of pluripotent states. This is also evident at the chromatin level, as the initial DNA demethylation that occurs in hPGCLCs is reversed in hEGCLCs. This new in vitro model provides a highly tractable system to study human pluripotent and early developmental transitions, including those driving germ cell tumorigenesis and epigenetic inheritance."],"study_type":["genotyping by high throughput sequencing"],"species":["Homo sapiens"],"pubmed_title":["High resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humans"],"pubmed_authors":["Sarah Stucchi, Gaja Matassa, Alessia Valenti, Lessly P. Sepulveda-Rincon, Camille Dion, Cristina Cheroni, Alessandro Vitriolo, Filippo Prazzoli, George Young, Marco Tullio Rigoli, Riccardo Nagni, Martina Ciprietti, Benedetta Muda, Zoe Heckhausen, Petra Hajkova, Nicolò Caporale, Giuseppe Testa, Harry G. Leitch","Gaja Matassa"],"additional_accession":[]},"is_claimable":false,"name":"Low-pass WGS of hiPSC and hEGCLC samples of CTL08A genotype","description":"Low-pass whole genome sequencing (WGS) of one sample of human induced pluripotent stem cells (hiPSCs) derived from the CTL08A male cell line and three samples of CTL08A human embryonic germ cell-like cells (hEGCLCs) at passage 10 after hPGCLC-hEGCLC conversion.","dates":{"release":"2026-02-10T00:00:00Z","modification":"2026-02-10T02:01:56.487Z","creation":"2025-09-02T20:34:41.277Z"},"accession":"E-MTAB-15528","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0002771","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1016/j.stemcr.2025.102746"]}}