biostudies-arrayexpressGaja MatassaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15142In this work, hEGCLC have been obtained for the first time from hPGCLC in defined and feeder-free conditions. To study epigenetic changes (in terms of DNA methylation) during the transition from a pluripotent stem cell state to a germ cell identity and back again, we profiled hiPSC, iMeLC, day 6 hPGCLC and hEGCLC by EMseq.biostudies-arrayexpressLibrary Construction - Libraries were synthesized from 200 ng purified DNA using NEBNext Enzymatic Methyl-seq (EM-seq) Library Preparation Kit (NEBNext, # 101977). Unmethylated Lambda phage DNA was spiked-in to evaluate the efficiency of bisulfite conversion. To generate target-enriched DNA libraries, Twist Targeted Methylation Sequencing Kit (TWIST Bioscience, #104181) was used, coupled with Twist Human Methylome Panel (TWIST Bioscience, #105521), according to the manufacturer's instructions (DOC-001224 REV 4.0). Libraries were pooled in equimolar quantities and the pool of libraries was amplified by qPCR. Quantification and validation of enriched libraries was performed by Qubit dsDNA High Sensitivity Quantitation Assay (Thermo Fisher Scientific, #Q33230) and Agilent Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, #5067-4626).Nucleic Acid Extraction - Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, #69504)Sample Collection - hiPSC, iMeLC and hEGCLC were detached form the culture dish using accutase, washed 2 times in PBS and stored at -80°C as snap-frozen pellets. Upon hPGCLC aggregates dissociation, hPGCLC were sorted in PBS and stored at -80°C as snap-frozen pellets.Sequencing - Libraries were sequenced on a NovaSeq6000 platform (Illumina) with at least 160X coverage.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The processed bam files are the results of trimming with Trim Galore v0.6.7 and alignment with bwa-meth v0.2.2, deduplication with MarkDuplicates (Picard v2.27.4), and removal of chrY reads for the legal constraints of the cell line.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000Primordial 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.methylation profiling by high throughput sequencingHomo sapiensHigh resolution multi-scale profiling of embryonic germ cell-like cell derivation reveals pluripotent state transitions in humansGiuseppe TestaSarah 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. LeitchGaja MatassaSarah StucchifalseEMseq of hiPSC, iMeLC, hPGCLC and hEGCLC of CTL08A genotypeIn this work, hEGCLC have been obtained for the first time from hPGCLC in defined and feeder-free conditions. To study epigenetic changes (in terms of DNA methylation) during the transition from a pluripotent stem cell state to a germ cell identity and back again, we profiled hiPSC, iMeLC, day 6 hPGCLC and hEGCLC by EMseq.2026-02-10T00:00:00Z2026-02-10T02:01:59.04Z2025-05-09T13:34:39.072ZE-MTAB-15142EFO_0002944EFO_0004170EFO_0002761EFO_0005518EFO_0003816EFO_000418410.1016/j.stemcr.2025.102746