{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/045/SRR31229745/SRR31229745.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/053/SRR31229753/SRR31229753_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/059/SRR31229759/SRR31229759_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/056/SRR31229756/SRR31229756_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/053/SRR31229753/SRR31229753_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/054/SRR31229754/SRR31229754.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/047/SRR31229747/SRR31229747_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/060/SRR31229760/SRR31229760.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/051/SRR31229751/SRR31229751.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/058/SRR31229758/SRR31229758.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/049/SRR31229749/SRR31229749.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/056/SRR31229756/SRR31229756_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/052/SRR31229752/SRR31229752.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/055/SRR31229755/SRR31229755.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/050/SRR31229750/SRR31229750_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/059/SRR31229759/SRR31229759_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/048/SRR31229748/SRR31229748.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/061/SRR31229761/SRR31229761.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/050/SRR31229750/SRR31229750_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/057/SRR31229757/SRR31229757.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/047/SRR31229747/SRR31229747_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR312/046/SRR31229746/SRR31229746.fastq.gz"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["University of Texas Southwestern Medical Center"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA1182275"],"scientific_name":["Homo sapiens"],"long_description":["Undifferentiated pleomorphic sarcoma (UPS) and related tumors are the most common type of soft tissue sarcoma. However, this spectrum of tumors has different etiologies with varying rates of metastasis and survival. Two dermal-based neoplasms in this class of pleomorphic sarcomas, atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS), are challenging to differentiate at initial biopsy but vary significantly in prognosis. We performed single-cell transcriptomics on five AFX and PDS biopsy specimens as well as both single-cell and spatial transcriptomics on one PDS excision specimen to better characterize these tumors. The top differential genes between AFX and PDS were predictive of overall survival in 17 other cancers included in the Human Protein Atlas. Of these genes, COL6A3 and BGN predicted overall survival and metastasis-free survival in independent cohorts of 46 and 38 UPS tumors, respectively. COL6A3 was most predictive of overall survival in UPS patients and outperformed an established sarcoma prognostic gene panel at predicting metastasis in UPS. Overall design: scRNAseq was performed with 10X Chromium Single Cell Gene Expression Flex. FFPE blocks for each sample were prepared per protocol CG000632 Rev C. Library preparation was conducted per protocol CG000691 Rev A. One million cells per sample were used for probe hybridization. 12,000 cells were loaded per sample. Libraries were sequenced on a Novaseq X 25B flowcell with PE 151bp reads and NextSeq2K, P3 with 28 and 90bp reads."],"tag":["xref:PubMed:39548577"],"repository":["ENA"],"description_synonyms":["d230, Biological Markers, Viral Marker, Surrogate Endpoints, Single-Cell RNAseq, Sc RNAseq, Clinical Markers, Laboratory, Clinical Marker, Single Cell Gene Expression Profiling, Biochemical, Gene, Endpoint, dTAFII250, ScRNA seq, Serum, EfW1, Gene Expression Profilings, Surrogate End Points, dmTAF[[II]]230, Transcript Expression Analysis, Surrogate Markers, Laboratory Markers, mRNA Differential Displays, Gene Expression Pattern Analysis, single-cell transcriptome sequencing, single-cell RNA-seq, dmTAF1, Taf230, Biological, Gene Expression Monitorings, Seqs, Analysis, Profilings, Seq, TAF250, Biomarker, Taf200, dTAF[[II]]250, Clinical, malignant fibrohistiocytic tumours, ScRNAseq, TFIID TAF250, Single-Cell Transcriptome Analysis, Analyses, cel, cell, Biological Marker, Taf1p, Transcriptomics, Single Cell RNAseq, Single Cell RNA Seq, Transcript Expression, Transcriptome Analysis, RNA Seq, Monitoring, ScRNA-seq, dTAF250, Single-Cell Transcriptome., Gene Expression Analysis, Immunologic Markers, Immune, Markers, Viral Markers, biological marker, RNA-Seq, TAF, Expression Analyses, Immunologic Marker, Biologic, Profiling, dTAF[[II]]230, TAF[[II]]250, Transcriptome, Viral, Single-Cell RNA-Seq, Surrogate Endpoint, undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma/high-grade spindle cell sarcoma, Single-Cell Gene Expression Profiling, Serum Markers, TAF200, Monitorings, scRNA-seq, End Point, l(3)84Ab, Biochemical Markers, BG:DS00004.13, TAFII-250, Single Cell Gene Expression Analysis, TAF250/230, Biologic Marker, Cell, Single-Cell, Single Cell Transcriptome Analysis, Immune Marker, dTAF230, Gene Expression, Differential Display, Sc-RNAseq, TAFII250, single cell RNA sequencing, Transcript Expression Analyses, Marker, Surrogate End Point, p230, TAF[[II]]250/230, TFIID, mRNA Differential Display, Biologic Markers, Taf[[II]]250, Gene Expression Monitoring, Single-Cell RNA, Serum Marker, Single-Cell Transcriptome Analyses, TAF[[II]]230, Transcriptome Profiling, End Points, mRNA, Surrogate, Transcriptome Profilings, Endpoints, malignant fibrohistiocytic tumors, TAF[II]250, Differential Displays, Immunologic, Laboratory Marker, CG17603, TAF[[II]], Single-Cell RNA Seq, Transcriptome Analyses, Surrogate Marker, Single-Cell Transcriptome, DmelCG17603, Gene Expression Analyses, Taf250, Biochemical Marker, SR3-5, RNAseq, Expression Analysis, TAF230, TAF1, Immune Markers"],"name_synonyms":["d230, Biological Markers, Viral Marker, Surrogate Endpoints, Single-Cell RNAseq, Sc RNAseq, Clinical Markers, Laboratory, Clinical Marker, Single Cell Gene Expression Profiling, Biochemical, Gene, Endpoint, dTAFII250, ScRNA seq, Serum, EfW1, Gene Expression Profilings, Surrogate End Points, dmTAF[[II]]230, Transcript Expression Analysis, Surrogate Markers, Laboratory Markers, mRNA Differential Displays, Gene Expression Pattern Analysis, single-cell transcriptome sequencing, single-cell RNA-seq, dmTAF1, Taf230, Biological, Gene Expression Monitorings, Seqs, Analysis, Profilings, Seq, TAF250, Biomarker, Taf200, dTAF[[II]]250, Clinical, malignant fibrohistiocytic tumours, ScRNAseq, TFIID TAF250, Single-Cell Transcriptome Analysis, Analyses, cel, cell, Biological Marker, Taf1p, Transcriptomics, Single Cell RNAseq, Single Cell RNA Seq, Transcript Expression, Transcriptome Analysis, RNA Seq, Monitoring, ScRNA-seq, dTAF250, Single-Cell Transcriptome., Gene Expression Analysis, Immunologic Markers, Immune, Markers, Viral Markers, biological marker, RNA-Seq, TAF, Expression Analyses, Immunologic Marker, Biologic, Profiling, dTAF[[II]]230, TAF[[II]]250, Transcriptome, Viral, Single-Cell RNA-Seq, Surrogate Endpoint, undifferentiated pleomorphic sarcoma/malignant fibrous histiocytoma/high-grade spindle cell sarcoma, Single-Cell Gene Expression Profiling, Serum Markers, TAF200, Monitorings, scRNA-seq, End Point, l(3)84Ab, Biochemical Markers, BG:DS00004.13, TAFII-250, Single Cell Gene Expression Analysis, TAF250/230, Biologic Marker, Cell, Single-Cell, Single Cell Transcriptome Analysis, Immune Marker, dTAF230, Gene Expression, Differential Display, Sc-RNAseq, TAFII250, single cell RNA sequencing, Transcript Expression Analyses, Marker, Surrogate End Point, p230, TAF[[II]]250/230, TFIID, mRNA Differential Display, Biologic Markers, Taf[[II]]250, Gene Expression Monitoring, Single-Cell RNA, Serum Marker, Single-Cell Transcriptome Analyses, TAF[[II]]230, Transcriptome Profiling, End Points, mRNA, Surrogate, Transcriptome Profilings, Endpoints, malignant fibrohistiocytic tumors, TAF[II]250, Differential Displays, Immunologic, Laboratory Marker, CG17603, TAF[[II]], Single-Cell RNA Seq, Transcriptome Analyses, Surrogate Marker, Single-Cell Transcriptome, DmelCG17603, Gene Expression Analyses, Taf250, Biochemical Marker, SR3-5, RNAseq, Expression Analysis, TAF230, TAF1, Immune Markers"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma [scRNA-Seq]","description":"Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma [scRNA-Seq]","dates":{"last_updated":"2025-09-24","first_public":"2024-11-11"},"accession":"PRJNA1182275","cross_references":{"GEO":["GSE281096"],"taxon":["9606"],"PubMed":["39548577"]}}