{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alessia Valenti"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15244"],"description":["In this work, hEGCLC have been obtained for the first time from hPGCLC in defined and feeder-free conditions. To study transcriptional changes during the transition from a pluripotent stem cell state to a germ cell identity and back again, we profiled hiPSC, iMeLC, day6 hPGCLC aggregates and hEGCLC by scRNAseq."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - scRNAseq libraries were prepared following Chromium Fixed RNA Profiling for Multiplexed Samples 10X protocol (CG000527-RevC).","Sequencing - A total of 7000 cells per sample were processed, pooling together 16 individually barcoded samples, after the hybridization step. A total of 8 cycles of PCR was used for library amplification. Libraries were sequenced on a NovaSeq6000 platform (Illumina). Using proper cluster density, a coverage of at least 25,000 reads/cell was obtained.","Nucleic Acid Extraction - Up to 1.5 million cells were taken from the cell suspension and processed according to 10X Fixation of Cells & Nuclei for Chromium Fixed RNA Profiling protocol (CG000478, Rev A)and stored at -80°C.","Sample Collection - hiPSC, iMeLC, hEGCLC were detached and dissociated into single-cell using Accutase (Sigma-Aldrich, #A6964). Day 6 hPGCLC aggregates were collected and dissociated into single-cells with Trypsin-EDTA. Single cells were resuspended in chilled 0.04% Bovine Serum Albumin (BSA, Merck, A9418-50G) in HBSS (ThermoFisher Scientific, #14025092), filtered by using 70-micron Flowmi cell strainers for 1000 ul tips (Merck, #BAH136800070) and counted with a Countess 3FL automatic cell counter (Thermo Fisher, #AMQUAF2000) using Trypan blue (Gibco, #15250062)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Single-cell RNA sequencing data came from 3 different run, multiplexed with the Flex protocol from 10X genomics. Data were aligned and demultiplexed against the probe reference file v1.0.0 from CellRanger using cellranger v7.0.0 with the exception of samples rep1_hPGCLC_aggregate and rep2_hPGCLC_aggregate  that were coming from a run which fastqs were aligned with cellranger 7.0.1. The output bam files for each demultiplexed sample are here uploaded."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"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":["RNA-seq of coding RNA from single cells"],"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":["Giuseppe Testa","Alessia Valenti","Sarah Stucchi, Lessly P. Sepulveda-Rincon, Camille Dion, Gaja Matassa, Alessia Valenti, Cristina Cheroni, Alessandro Vitriolo, Filippo Prazzoli, George Young, Marco Tullio Rigoli, Riccardo Nagni, Martina Ciprietti, Benedetta Muda, Zoe Heckhausen, Petra Hajkova, Nicolo` Caporale, Giuseppe Testa and Harry G. Leitch","Sarah Stucchi"],"additional_accession":[]},"is_claimable":false,"name":"scRNAseq of hiPSC, iMeLC, hPGCLC aggregates and hEGCLC of CTL08A genotype","description":"In this work, hEGCLC have been obtained for the first time from hPGCLC in defined and feeder-free conditions. To study transcriptional changes during the transition from a pluripotent stem cell state to a germ cell identity and back again, we profiled hiPSC, iMeLC, day6 hPGCLC aggregates and hEGCLC by scRNAseq.","dates":{"release":"2026-02-10T00:00:00Z","modification":"2026-02-10T02:01:58.944Z","creation":"2025-06-13T12:09:58.668Z"},"accession":"E-MTAB-15244","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1016/j.stemcr.2025.102746"]}}