{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR313/014/SRR31302014/SRR31302014_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR313/014/SRR31302014/SRR31302014_1.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/PRJNA1184336"],"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: 10X Visium spatial transcriptomics was performed on a PDS excision specimen by CD Genomics"],"repository":["ENA"],"description_synonyms":["d230, Biological Markers, Viral Marker, Sarcoma of the Soft Tissue and Bone, Surrogate Endpoints, Clinical Markers, Laboratory, Clinical Marker, MAL NEO SOFT TISSUE NEC, Spindle Cell Sarcomas, Biochemical, Gene, Endpoint, dTAFII250, Serum, EfW1, Gene Expression Profilings, Surrogate End Points, dmTAF[[II]]230, Transcript Expression Analysis, Surrogate Markers, site unspecified, Laboratory Markers, mRNA Differential Displays, unspecified, Gene Expression Pattern Analysis, Soft Tissue Sarcoma, Sarcoma of Soft Tissue, dmTAF1, Taf230, Biological, Malignant neoplasm of soft tissue, Gene Expression Monitorings, [M]Sarcoma NOS (morphologic abnormality), Analysis, Profilings, tumour of soft tissue and skeleton, Sarcoma of Soft Tissue and Bone, MAL NEO SOFT TIS PELVIS, TAF250, Malignant neoplasm of connective and other soft tissue of upper limb, Biomarker, Sarcomas, Malignant Tumor of the Soft Tissue, MAL NEO SOFT TIS ABDOMEN, Malignant neoplasm of connective and other soft tissue of head, Taf200, MAL NEOPL TRUNK NOS., dTAF[[II]]250, Clinical, TFIID TAF250, Analyses, cel, cell, Biological Marker, MAL NEO SOFT TIS THORAX, Malignant neoplasm of connective and other soft tissue of abdomen, Taf1p, Transcriptomics, tumor of soft tissue and skeleton, Transcript Expression, Transcriptome Analysis, high grade, Monitoring, dTAF250, Gene Expression Analysis, Sarcoma, Immunologic Markers, Immune, Markers, Malignant neoplasm of soft tissue (disorder), no ICD-O subtype (morphologic abnormality), Viral Markers, Malignant tumor of soft tissue, Malignant Neoplasm of the Soft Tissue, face, biological marker, Spindle Cell Sarcoma, TAF, Expression Analyses, Immunologic Marker, Biologic, connective and soft tissue neoplasm, MAL NEO SOFT TISSUE ARM, Connective Tissue Sarcoma, Malignant Soft Tissue Tumor, Profiling, MAL NEO SOFT TISSUE LEG, sarcoma, dTAF[[II]]230, TAF[[II]]250, Transcriptome, Viral, Mesenchymal tumor, Surrogate Endpoint, malignant, Serum Markers, Malignant neoplasm of connective and other soft tissue of lower limb, TAF200, Monitorings, End Point, l(3)84Ab, Biochemical Markers, BG:DS00004.13, TAFII-250, TAF250/230, Biologic Marker, Cell, Malignant neoplasm of connective and other soft tissue of thorax, Malignant neoplasm of other specified sites of connective and other soft tissue, Immune Marker, dTAF230, [M]Sarcoma NOS, Gene Expression, Differential Display, Sarcoma of the Soft Tissue, Malignant neoplasm of connective and other soft tissue, TAFII250, Transcript Expression Analyses, Marker, Surrogate End Point, including shoulder, p230, Epithelioid Sarcomas, Malignant tumour of soft tissue, MAL NEO SOFT TISSUE HEAD, Soft tissue tumour, TAF[[II]]250/230, TFIID, NOS, Malignant mesenchymal tumour, mRNA Differential Display, Epithelioid, Biologic Markers, Taf[[II]]250, Malignant neoplasm of connective and other soft tissue (disorder), Gene Expression Monitoring, Serum Marker, TAF[[II]]230, Spindle Cell, MAL NEO SOFT TISSUE NOS, Transcriptome Profiling, End Points, mRNA, Surrogate, Transcriptome Profilings, including hip, Endpoints, and neck, Soft Tissue Sarcomas, TAF[II]250, Malignant neoplasm of connective and other soft tissue of trunk, Differential Displays, Immunologic, Laboratory Marker, CG17603, TAF[[II]], Malignant Soft Tissue Neoplasm, Transcriptome Analyses, Surrogate Marker, DmelCG17603, Gene Expression Analyses, no ICD-O subtype, Taf250, Biochemical Marker, SR3-5, Epithelioid Sarcoma, Expression Analysis, Malignant neoplasm of connective and other soft tissue of pelvis, TAF230, Soft Tissue, TAF1, Immune Markers"],"name_synonyms":["d230, Biological Markers, Viral Marker, Sarcoma of the Soft Tissue and Bone, Surrogate Endpoints, Clinical Markers, Laboratory, Clinical Marker, MAL NEO SOFT TISSUE NEC, Spindle Cell Sarcomas, Biochemical, Gene, Endpoint, dTAFII250, Serum, EfW1, Gene Expression Profilings, Surrogate End Points, dmTAF[[II]]230, Transcript Expression Analysis, Surrogate Markers, site unspecified, Laboratory Markers, mRNA Differential Displays, unspecified, Gene Expression Pattern Analysis, Soft Tissue Sarcoma, Sarcoma of Soft Tissue, dmTAF1, Taf230, Biological, Malignant neoplasm of soft tissue, Gene Expression Monitorings, [M]Sarcoma NOS (morphologic abnormality), Analysis, Profilings, tumour of soft tissue and skeleton, Sarcoma of Soft Tissue and Bone, MAL NEO SOFT TIS PELVIS, TAF250, Malignant neoplasm of connective and other soft tissue of upper limb, Biomarker, Sarcomas, Malignant Tumor of the Soft Tissue, MAL NEO SOFT TIS ABDOMEN, Malignant neoplasm of connective and other soft tissue of head, Taf200, MAL NEOPL TRUNK NOS., dTAF[[II]]250, Clinical, TFIID TAF250, Analyses, cel, cell, Biological Marker, MAL NEO SOFT TIS THORAX, Malignant neoplasm of connective and other soft tissue of abdomen, Taf1p, Transcriptomics, tumor of soft tissue and skeleton, Transcript Expression, Transcriptome Analysis, high grade, Monitoring, dTAF250, Gene Expression Analysis, Sarcoma, Immunologic Markers, Immune, Markers, Malignant neoplasm of soft tissue (disorder), no ICD-O subtype (morphologic abnormality), Viral Markers, Malignant tumor of soft tissue, Malignant Neoplasm of the Soft Tissue, face, biological marker, Spindle Cell Sarcoma, TAF, Expression Analyses, Immunologic Marker, Biologic, connective and soft tissue neoplasm, MAL NEO SOFT TISSUE ARM, Connective Tissue Sarcoma, Malignant Soft Tissue Tumor, Profiling, MAL NEO SOFT TISSUE LEG, sarcoma, dTAF[[II]]230, TAF[[II]]250, Transcriptome, Viral, Mesenchymal tumor, Surrogate Endpoint, malignant, Serum Markers, Malignant neoplasm of connective and other soft tissue of lower limb, TAF200, Monitorings, End Point, l(3)84Ab, Biochemical Markers, BG:DS00004.13, TAFII-250, TAF250/230, Biologic Marker, Cell, Malignant neoplasm of connective and other soft tissue of thorax, Malignant neoplasm of other specified sites of connective and other soft tissue, Immune Marker, dTAF230, [M]Sarcoma NOS, Gene Expression, Differential Display, Sarcoma of the Soft Tissue, Malignant neoplasm of connective and other soft tissue, TAFII250, Transcript Expression Analyses, Marker, Surrogate End Point, including shoulder, p230, Epithelioid Sarcomas, Malignant tumour of soft tissue, MAL NEO SOFT TISSUE HEAD, Soft tissue tumour, TAF[[II]]250/230, TFIID, NOS, Malignant mesenchymal tumour, mRNA Differential Display, Epithelioid, Biologic Markers, Taf[[II]]250, Malignant neoplasm of connective and other soft tissue (disorder), Gene Expression Monitoring, Serum Marker, TAF[[II]]230, Spindle Cell, MAL NEO SOFT TISSUE NOS, Transcriptome Profiling, End Points, mRNA, Surrogate, Transcriptome Profilings, including hip, Endpoints, and neck, Soft Tissue Sarcomas, TAF[II]250, Malignant neoplasm of connective and other soft tissue of trunk, Differential Displays, Immunologic, Laboratory Marker, CG17603, TAF[[II]], Malignant Soft Tissue Neoplasm, Transcriptome Analyses, Surrogate Marker, DmelCG17603, Gene Expression Analyses, no ICD-O subtype, Taf250, Biochemical Marker, SR3-5, Epithelioid Sarcoma, Expression Analysis, Malignant neoplasm of connective and other soft tissue of pelvis, TAF230, Soft Tissue, TAF1, Immune Markers"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma","description":"Single-cell and spatial transcriptomics identify COL6A3 as a prognostic biomarker in undifferentiated pleomorphic sarcoma","dates":{"last_updated":"2025-09-24","first_public":"2024-11-13"},"accession":"PRJNA1184336","cross_references":{"GEO":["GSE281529"],"taxon":["9606"]}}