{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"study_type":["Other"],"full_dataset_link":["https://ega-archive.org/studies/EGAS00001003452"],"host":["EGA"],"description":["EGA study EGAS00001003452"],"dataset_title":["Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers"],"repository":["EGA"],"category":["restricted"],"name_synonyms":["Taf[[II]]250, Taf200, dTAF[[II]]230, TAF[[II]]250, d230, dTAF[[II]]250, TAF[[II]]230, human being, Man (Taxonomy), TFIID TAF250, cel, cell, Modern, TAF200, l(3)84Ab, dTAFII250, Taf1p, TAF[II]250, BG:DS00004.13, TAFII-250, CG17603, TAF250/230, TAF[[II]], EfW1, cell_type, Cell, dTAF230, Human, dTAF250, dmTAF[[II]]230, TAFII250, DmelCG17603, Taf250, Homo sapiens, dmTAF1, SR3-5, Taf230, p230, Modern Man, TAF[[II]]250/230, TFIID, TAF, human., Man, TAF230, TAF250, TAF1"],"description_synonyms":["WASLBP, scale tissue, Materials, RNA Sequence Determination, PhrB photolyase activity, determination, acetylglucosaminyltransferase-like protein, Sequence Determination, Nodular Histiocytic Lymphomas, RNA Sequence, Mbp1, ScRNA seq, Measure, Tumor, pigmented epithelium, temporal, Small Follicular Center-Cell Lymphoma, Brill-Symmers, Small Cleaved-Cell, Wasbp, dmTAF[[II]]230, Follicular Large-Cell Lymphomas, single-cell RNA-seq, Seqs, 3, NUP96, Analysis, Mixed-Cell Lymphoma, myd, epithelium, Lymphomas, Follicular, Seq, Mixed Small and Large Cell, Histiocytic Lymphoma, ScRNAseq, TFIID TAF250, Single-Cell Transcriptome Analysis, like-acetylglucosaminyltransferase, reference sample, Analyses, cel, Determination, Tissue, pigmented retina, Nodular Large Follicular Center-Cell Lymphoma, Weights, Mbp-1, Small Follicular Center Cell, Follicular Mixed-Cell Lymphoma, Sequence Determinations, DNA cyclobutane dipyrimidine photolyase activity, SUPPRESSOR OF AUXIN RESISTANCE 3, Large Cell Lymphoma, Large Follicular Center Cell, DIP, malignant neoplasm, Medicine, Mixed Lymphocytic-Histiocytic, Giant Follicular, Malignancies, Tumors, PRE, Giant Follicular Lymphoma, dTAF[[II]]230, Wiskott-Aldrich syndrome protein-interacting protein, Small Lymphoid, anatomical protrusion, gyltl1b-b, Follicular Large Cell, Single-Cell Gene Expression Profiling, WISH, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, TAF200, scRNA-seq, TAFII-250, TAF250/230, Single-Cell, Determinations, TAFII250, single cell RNA sequencing, Experimental, Benign, batch, retinal pigment, Giant Follicular Lymphomas, WASP-interacting SH3-domain protein, MDDGA6, mKIAA0609, DIP-1, dipyrimidine photolyase (photosensitive), Nodular Lymphomas, Genetic Materials, Nodular Histiocytic Lymphoma, KIAA0609, retinal pigment layer, Nodular Lymphoma, Genetic Material, acetylglucosaminyltransferase-like 1A, Large-Cell Lymphoma, fg, Single-Cell RNA, Epistemology, gyltl1b, SH3 adapter protein SPIN90, N-WASP-binding protein, mdc1d, Benign Neoplasms, CG17603, TAF[[II]], Single-Cell RNA Seq, LARGE_HUMAN, cell_type, Malignant Neoplasms, Follicular Mixed-Cell Lymphomas, Phenotypes, MDC1D, Brill-Symmers Disease, phr A photolyase activity, DNA-photoreactivating enzyme, lymphoma, enr, Nodular Histiocytic, Taf250, Patient, Wiskott-Aldrich syndrome protein-binding protein, Material, spine, SR3-5, RNAseq, Lymphoma, Follicular Large-Cell, SPIN90, Cistron, Follicular Large Cell Lymphoma, Measures and Weights, Poorly Differentiated, Dia-interacting protein 1, TAF230, 54 kDa VacA-interacting protein, Follicular Mixed Cell Lymphoma, d230, DIP1, Large Follicular Center-Cell, Single-Cell RNAseq, Sc RNAseq, Single Cell Gene Expression Profiling, Neoplasms, Benign Neoplasm, Gene, dTAFII250, photoreactivating enzyme activity, EfW1, Malignant, 54 kDa vimentin-interacting protein, LARGE1, froggy, Biomedical, Gyltl1a, protrusion, Nodular Large Follicular Center Cell Lymphoma, single-cell transcriptome sequencing, Investigative, Large Lymphoid Lymphoma, dmTAF1, Taf230, Small Cleaved Cell Lymphoma, Medical Research, Cell., stratum pigmentosa retinae, Medical, TAF250, 90 kDa N-WASP-interacting protein, Lymphocytic, Follicular Lymphomas, Taf200, MOS3, dTAF[[II]]250, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, Genetic, PRECOCIOUS, Malignancy, Research, cell, MDDGB6, Mixed-Cell Lymphomas, F23A5.3, Measures, Taf1p, Single Cell RNAseq, LARGE, Single Cell RNA Seq, Transcriptome Analysis, RNA Seq, Mixed Cell Lymphoma, Sequencing, Follicular Large-Cell Lymphoma, ScRNA-seq, Small Follicular Center-Cell, Neoplasias, dTAF250, BPFD#36, Large-Cell, Mixed Small and Large Lymphoid, RNA Sequence Analyses, Histiocytic Lymphomas, Poorly-Differentiated, Clients, Nodular, Investigational Medicine, RNA Sequencing, malignant ovarian serous tumour, Follicular Lymphoma, RNA-Seq, TAF, serous ovarian cancer, F23A5_3, incidence, Controlled, Sequence Analyses, Cancer, VIP54, RNA, Controlling, Disease, TAF[[II]]250, Single-Cell RNA-Seq, Malignant Neoplasm, RNA Sequence Determinations, follicular, Large-Cell Lymphomas, Follicular Mixed-Cell, l(3)84Ab, BG:DS00004.13, Small and Large Cleaved-Cell, Single Cell Gene Expression Analysis, Cistrons, Client, Cell, Single Cell Transcriptome Analysis, AF3p21, dTAF230, Sc-RNAseq, Investigative Medicine, Small and Large Cleaved Cell, MODIFIER OF SNC1, Mixed Lymphocytic Histiocytic, MT, p230, chemical analysis, deoxyribonucleic photolyase activity, Neoplasm, TAF[[II]]250/230, TFIID, Mixed Cell, Brill Symmers Disease, scales, Large Cell, Investigational, Giant, Taf[[II]]250, Single-Cell Transcriptome Analyses, primary cancer, RPE, TAF[[II]]230, distinct, Scales, photolyase activity, Histiocytic, Experimental Medicine, TAF[II]250, patient, 90 kDa SH3 protein interacting with Nck, Cancers, Small Cleaved Cell, Transcriptome Analyses, malignant tumor, p. pigmentosa retinae, Grade 1, Grade 2, Grade 3, Single-Cell Transcriptome, DmelCG17603, like-glycosyltransferase, Lymphocytic Lymphoma, Small Follicular Center Cell Lymphoma, ORF1, RNA Sequence Analysis, deoxyribonucleate pyrimidine dimer lyase (photosensitive), assay, Diaphanous protein-interacting protein, AF3P21, Large Lymphoid, Small Cleaved-Cell Lymphoma, Neoplasia, Mixed-Cell, glycosyltransferase-like protein LARGE1, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers","description":"Single-cell RNA sequencing (scRNA-seq) has transformed biomedical research, enabling decomposition of complex tissues into disaggregated, functionally distinct cell types. For many applications, investigators wish to identify cell types with known marker genes. Typically, such cell type assignments are performed through unsupervised clustering followed by manual annotation based on these marker genes, or via \"mapping\" procedures to existing data. However, the manual interpretation required in the former case scales poorly to large datasets, which are also often prone to batch effects, while existing data for purified cell types must be available for the latter. Furthermore, unsupervised clustering can be error-prone, leading to under- and over- clustering of the cell types of interest. To overcome these issues we present CellAssign, a probabilistic model that leverages prior knowledge of cell type marker genes to annotate scRNA-seq data into pre-defined and de novo cell types. CellAssign automates the process of assigning cells in a highly scalable manner across large datasets while simultaneously controlling for batch and patient effects. We demonstrate the analytical advantages of CellAssign through extensive simulations and exemplify real-world utility to profile the spatial dynamics of high-grade serous ovarian cancer and the temporal dynamics of follicular lymphoma. Our analysis reveals subclonal malignant phenotypes and points towards an evolutionary interplay between immune and cancer cell populations with cancer cells escaping immune recognition.","dates":{"updated":"2022-11-22 12:10:03"},"accession":"EGAS00001003452","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAD00001004585","EGAC00000000011"]}}