{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2500 (ILLUMINA), Illumina HiSeq 4000 (ILLUMINA)"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003337"],"sample_count":["5063"],"description":["EGA dataset EGAD00001003337"],"repository":["EGA"],"title":["Single-cell RNA sequencing on 5063 single T cells from six hepatocellular carcinoma patients"],"pubmed_abstract":["Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8<sup>+</sup> T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8<sup>+</sup> T cells and Tregs and represses the CD8<sup>+</sup> T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers."],"pubmed_title":["Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing."],"pubmed_authors":["Zheng Chunhong C, Zheng Liangtao L, Yoo Jae-Kwang JK, Guo Huahu H, Zhang Yuanyuan Y, Guo Xinyi X, Kang Boxi B, Hu Ruozhen R, Huang Julie Y JY, Zhang Qiming Q, Liu Zhouzerui Z, Dong Minghui M, Hu Xueda X, Ouyang Wenjun W, Peng Jirun J, Zhang Zemin Z"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"description_synonyms":["Carcinoma, RNA, Ribonucleic, Liver, Malignant Neoplasm, whole blood, ribose nucleic acid, T-lymphocyte receptor complex, Blood, Neoplasms, Benign Neoplasm, ribonucleic acids, Cell Carcinoma, Liver Cell, RNS, adult hepatoma, Tumor, Hepatomas, Malignant, Liver Cell Carcinoma, Client, Cell, Cell Carcinomas, Responder protein Smok-Tcr, method, 2.7.11.1, Benign, TCR complex, HCC, Liver Cell Carcinomas, yeast nucleic acid, PBMC, method used in an experiment, Ribonukleinsaeure, Neoplasm, Gene Products, Adult Liver Cancer, pentosenucleic acids, Ribonucleic acids, Adult Liver, Non Polyadenylated, RNA Gene Products, T lymphocyte receptor complex, Carcinomas, average, ribonucleic acid, Acid, TCR, Tcr, Peripheral Blood, Adult Liver Cancers, Hepatocellular carcinoma, Malignancy, Liver Cancer, Hepatoma, Non Polyadenylated RNA, Tissue, Non-Polyadenylated, adult primary hepatocellular carcinoma, Liver Cancers, Benign Neoplasms, Cancers, Ribonucleic Acid, Adult, study protocol, Malignant Neoplasms, Hepatocellular Carcinoma, SmokTcr., Reticuloendothelial System, plan specification, Non-Polyadenylated RNA, Neoplasias, Patient, Clients, PBMCs, Hepatocellular, Dominant negative form of Smok, Malignancies, T-cell receptor complex, Hepatocellular Carcinomas, Neoplasia, Cancer, Tumors"],"pubmed_title_synonyms":["dTAF[[II]]230, TAF[[II]]250, d230, NEOPL LIVER, Liver, Hepatic Cancers, primary tumour of the liver, resectable malignant neoplasm of the liver, primary tumor of the liver, Neoplasms, infiltrating, Cancer of Liver, primary cancer of liver, TAF200, liver Cancers, l(3)84Ab, dTAFII250, adult hepatoma, BG:DS00004.13, hepatic, TAFII-250, Hepatic Neoplasm, TAF250/230, EfW1, hepatocellular carcinoma plus intrahepatic cholangiocarcinoma, Cell, primary liver cancer, dTAF230, dmTAF[[II]]230, liver, TAFII250, dmTAF1, Taf230, p230, Liver Neoplasm, Neoplasm, TAF[[II]]250/230, TFIID, primary, TAF250, not specified as primary or secondary, Taf[[II]]250, Taf200, ca liver - primary, Hepatic Cancer, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, Liver Cancer, primary malignant neoplasm of Liver, cel, cell, non-resectable primary hepatic malignant neoplasm, Cancer of the liver, adult primary hepatocellular carcinoma, Liver Cancers, Hepatic Neoplasms, Taf1p, TAF[II]250, Cancers, malignant neoplasm of liver, malignant tumor of liver, hepatic cancer, CG17603, TAF[[II]], neoplasm of liver, dTAF250, malignant hepato-biliary neoplasm, Resectable malignant neoplasm of Liver, DmelCG17603, primary malignant neoplasm of liver, TAF1., Ca liver - primary, Taf250, SR3-5, Hepatocellular Cancers, Hepatocellular, LIVER NEOPL, Hepatic, Cancer of liver, Cancer of the Liver, hepatic neoplasm, TAF, Hepatocellular Cancer, TAF230, Cancer, liver Cancer"],"pubmed_abstract_synonyms":["Materials, single-organism developmental process, FON1, Blood, postnatal development, Gene Expression Profile, growth and development, adult hepatoma, Profiles, Tumor, FLORAL ORGAN NUMBER 1, Hepatomas, Liver Cell Carcinoma, brl, dmTAF[[II]]230, Readability, single-cell RNA-seq, SUP, CG9063, IKKg, KEY, Key, average, DRCTNNB1A, TFIID TAF250, cel, Tissue, Bdr, adult primary hepatocellular carcinoma, HLD5, Adult, Super protein, BcDNA:GH03694, Signatures, sp, SNAP-25, Hepatocellular Carcinoma, Expression Signature, Transcriptomes, Malignancies, Lymphoid, DmelCG9063, Tumors, Carcinoma, dTAF[[II]]230, Liver, Expression Profiles, scRNA-seq, TAF200, Liver Cell, TAFII-250, TAF250/230, Expanded, Gene Expression, DmIKKgamma, single cell RNA sequencing, TAFII250, Benign, HCC, dIKK, 1270, Expression Signatures, Kenny, GENA70, Genetic Materials, Lymphoid Cell, Adult Liver, Expression Profile, Genetic Material, Transcriptome Profiles, Carcinomas, Immunotherapies, Hepatoma, p32, BcDNAGH03694, IKK-gamma, expanded, Ex, Benign Neoplasms, CG17603, TAF[[II]], 3L6, SmokTcr, Malignant Neoplasms, DmelCG16910, Patient, Taf250, enlarged, rich, Material, SR3-5, PBMCs, Cells, Dominant negative form of Smok, l(2)ey, Cistron, T-cell receptor complex, Hepatocellular Carcinomas, other neoplasm, TAF230, FLORAL DEFECTIVE 10, HYCC1, big, Understanding., d230, Transcriptome Profile, Neoplasms, infiltrating, Benign Neoplasm, Cell Carcinoma, Gene, dTAFII250, SUPERMAN, Malignant, EfW1, dIKK-gamma, Cell Carcinomas, Responder protein Smok-Tcr, large, DmelCG4114, single-cell transcriptome sequencing, Liver Cell Carcinomas, dmTAF1, Taf230, DmIKK-gamma, PBMC, Adult Liver Cancer, dmIKKgamma, IKK[[gamma]], MAL, TAF250, Taf200, dTAF[[II]]250, Genetic, Malignancy, Liver Cancer, cell, Profile, Liver Cancers, Taf1p, Neoplasias, dTAF250, Mif1, IKK, Clients, great, TAF, Lymphocyte, Cancer, TAF[[II]]250, Transcriptome, Malignant Neoplasm, whole blood, T-lymphocyte receptor complex, CG4114, Leu2, l(3)84Ab, BG:DS00004.13, Synaptosomal-associated 25 kDa protein, Cistrons, Client, Cell, dTAF230, development, IKKgamma, 2.7.11.1, TCR complex, p230, Gene Expression Signatures, Neoplasm, TAF[[II]]250/230, TFIID, Gene Expression Signature, Lymphoid Cells, T lymphocyte receptor complex, Taf[[II]]250, TCR, Tcr, TAF[[II]]230, Peripheral Blood, Adult Liver Cancers, Hepatocellular carcinoma, Dmikkgamma, postnatal growth, TAF[II]250, FLO10, Cancers, CG16910, HERP, Reticuloendothelial System, l(2)01270, DmelCG17603, Gene Expression Profiles, SNAP, Hepatocellular, CD8, Signature, growth, Neoplasia, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-BIOPIC-16-05-2017-14:34:15:534-498 - samples","description":"T cells isolated from peripheral blood, tumors and adjacent normal tissues from six hepatocellular carcinoma patients. SmartSeq2 and Tang2009 protocol were used to amplify RNA from single T cells. High depth enables simultaneously expression profiling and TCR assembling.","dates":{"updated":"2018-01-26 14:50:52"},"accession":"EGAD00001003337","cross_references":{"TAXONOMY":["9606"],"pubmed":["28622514"],"EGA":["EGAC00001000551","EGAS00001002072"]}}