{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Artem Toropov"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15748"],"description":["This study investigates the cellular heterogeneity of Synovial Sarcoma (SyS), an aggressive cancer defined by the SS18-SSX fusion oncogene and exhibiting diverse clinical behavior. We used single-cell RNA sequencing (scRNA-seq) on tumor samples from 16 patients to deconstruct this diversity at high resolution, aiming to characterize molecular subtypes and elucidate how their unique transcriptional programs influence key oncogenic processes like immune evasion and chemoresistance. The experimental workflow involved processing surgically resected tumors into fixed single-cell suspensions, followed by library construction using the 10x Genomics Chromium Fixed RNA Profiling platform and sequencing with the Genolab M platform."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The study included 16 male and female patients aged 19-77, with the diagnosis of primary or recurring SyS (13 monophasic and 3 biphasic cases) and with or without neoadjuvant treatment. Surgically removed tumor samples (20-25 mg) were used to perform scRNA-seq. The study was conducted in accordance with the Declaration of Helsinki and approved by The Ethics Committee of N.N. Blokhin National Medical Research Center of Oncology (27 October 2020; Approval number: 2020-42). Informed consent for the study and the future publication has been obtained from the patients.","Nucleic Acid Extraction - The fixation and dissociation of tumor samples were performed according to the Tissue Fixation & Dissociation Protocol for Chromium Fixed RNA Profiling (10x Genomics, USA) using the DCS-400 single cell suspension dissociator and the Tumor Enzymatic Dissociation Kit  (RWD Life Science, China). After the dissociation, the cells were counted with acridine orange/propidium iodide staining buffer (Logos Bioscience, Korea) on the LUNA-FL Dual Fluorescence Cell Counter (Logos Bioscience, Korea). The dissociated cell suspension was stored at –80℃ with 275 µl of 50% glycerol (Central Drug House Ltd, India) and 100 µl of Enhancer solution (10x Genomics, USA). Before the Chromium Fixed RNA Profiling, cells were thawed, centrifuged, resuspended in 0.5x PBS (Diagene, Switzerland) with 0.02% BSA (Dia-M, Russia), and counted again. For each SyS tumor sample, 8000 cells were taken into the scRNA-seq.","Sequencing - The sequencing was performed on the Genolab M platform (GeneMind Biosciences, China) using 28 cycles (Read 1) and 90 cycles (Read 2).","Library Construction - The single-cell transcriptomic libraries were constructed in accordance with the Chromium Fixed RNA Protocol using  the Chromium iX/X controller (10x Genomics, USA). The PCR amplification was done on the QuantGene 9600 machine (Bioer Technology, China)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Raw scRNA-seq reads were demultiplexed and aligned to the GRCh38-2020-A reference genome using the Cell Ranger pipeline v.7.1.0.  NOTE: Raw FASTQ files were generated from demultiplexed BAM files using the cellranger bamtofastq tool v1.4.1.","Data Transformation - The processed files represent cellranger multi output files for each sample, containing only detected cell-associated (filtered) barcodes."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Genolab M"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Revealing novel subtypes of synovial sarcoma through single cell transcriptomics"],"pubmed_authors":["Artem Toropov","Artem L. Toropov, Elena E. Kopantseva, Alexander V. Ikonnikov, Maxim E. Menyailo, Timur I. Fetisov, Anna M. Stroganova, Daria A. Meshkova, Nikolay A. Kozlov, Polina A. Shtompel, Sofya A. Khazanova, Ekaterina A. Trapeznikova, Kirill I. Kirsanov,  Anastasia A. Tararykova, Marianna G. Yakubovskaya, Evgeny V. Denisov"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell transcriptomic profiling of 16 synovial sarcoma tumors","description":"This study investigates the cellular heterogeneity of Synovial Sarcoma (SyS), an aggressive cancer defined by the SS18-SSX fusion oncogene and exhibiting diverse clinical behavior. We used single-cell RNA sequencing (scRNA-seq) on tumor samples from 16 patients to deconstruct this diversity at high resolution, aiming to characterize molecular subtypes and elucidate how their unique transcriptional programs influence key oncogenic processes like immune evasion and chemoresistance. The experimental workflow involved processing surgically resected tumors into fixed single-cell suspensions, followed by library construction using the 10x Genomics Chromium Fixed RNA Profiling platform and sequencing with the Genolab M platform.","dates":{"release":"2025-10-16T00:00:00Z","modification":"2026-05-27T14:52:24.908Z","creation":"2025-10-16T10:54:31.403Z"},"accession":"E-MTAB-15748","cross_references":{"ENA":["ERP182287"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}