{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Xianwen Ren"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000551"],"host":["EGA"],"description":["EGA DAC EGAC00001000551"],"repository":["EGA"],"email":["renxwise@pku.edu.cn"],"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":["DmelCG7399, Non-phenylketonuria hyperphenylalaninemia, Thymus-Dependent Lymphocytes, anatomical protrusion, oligophrenia Phenylpyruvica, Activity, TRH, Trh, Laboratory, imbecilitus phenylpyruvica, \"PKU\" EXACT [MTH:NOCODE], PKU1, Research Priorities, pah, T-Lymphocyte, phenylketonuria, Cell, protrusion, Phenylketonuria, Priority, DTPH, T Lymphocyte, T-Cell, Research Activities, \"Phenylketonuria [PKU]\" EXACT [ICD9CM_2006:270.1], University, CG7399, Research Activity, HPA, immature T cell, Laboratory Research, T lymphocyte, PKU, \"PKU\" EXACT [CSP2005:1849-1234], maternal, Research and Development, Priorities, T-cell, Research, T-Cells, TPH, Tph, Thymus-Dependent, non-PKU mild, bu, T, Lymphocytes, phenylpyruvic oligophrenia, \"PKU\" EXACT [MTHICD9_2006:270.1], oligophrenia phenylpyruvica, T-lymphocyte, Research Activities., Thymus-Dependent Lymphocyte, Activities, T Cells, T cell, Peking, spine, mature T cell, Cells, \"phenylalaninemia\" EXACT [CSP2005:1849-1177], \"Phenylketonuria\" EXACT [SNOMEDCT_2005_07_31:154735006], T Cell, Development and Research, PAH, Pah, Research Priority, PH, T Lymphocytes, Thymus Dependent Lymphocytes, Lymphocyte, \"Phenylketonuria\" EXACT [SNOMEDCT_2005_07_31:190687004]"],"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":["HYCC1, big, Understanding., d230, Materials, single-organism developmental process, RNA Sequence Determination, Transcriptome Profile, Sequence Determination, FON1, Neoplasms, Blood, postnatal development, RNA Sequence, infiltrating, Benign Neoplasm, Gene Expression Profile, Cell Carcinoma, Gene, dTAFII250, growth and development, SUPERMAN, adult hepatoma, Profiles, Tumor, FLORAL ORGAN NUMBER 1, Hepatomas, Malignant, EfW1, Liver Cell Carcinoma, brl, dmTAF[[II]]230, Cell Carcinomas, Responder protein Smok-Tcr, large, Readability, DmelCG4114, dmTAF1, Liver Cell Carcinomas, Taf230, PBMC, SUP, Adult Liver Cancer, Analysis, MAL, TAF250, average, Taf200, DRCTNNB1A, dTAF[[II]]250, Genetic, TFIID TAF250, Malignancy, Analyses, Liver Cancer, cel, Determination, cell, Profile, Tissue, Bdr, adult primary hepatocellular carcinoma, Liver Cancers, HLD5, Taf1p, Adult, Super protein, Sequence Determinations, Signatures, Sequencing, sp, SNAP-25, Hepatocellular Carcinoma, Neoplasias, dTAF250, Mif1, RNA Sequence Analyses, Expression Signature, Clients, great, Transcriptomes, RNA Sequencing, Malignancies, Lymphoid, TAF, Lymphocyte, Cancer, Tumors, Sequence Analyses, Carcinoma, RNA, dTAF[[II]]230, TAF[[II]]250, Liver, Transcriptome, Malignant Neoplasm, whole blood, RNA Sequence Determinations, T-lymphocyte receptor complex, Expression Profiles, CG4114, TAF200, Leu2, l(3)84Ab, Liver Cell, BG:DS00004.13, Synaptosomal-associated 25 kDa protein, TAFII-250, TAF250/230, Cistrons, Client, Cell, Determinations, Expanded, dTAF230, development, Gene Expression, TAFII250, 2.7.11.1, Benign, TCR complex, HCC, p230, 1270, Expression Signatures, Gene Expression Signatures, Neoplasm, TAF[[II]]250/230, TFIID, GENA70, Genetic Materials, Lymphoid Cell, Adult Liver, Gene Expression Signature, Expression Profile, Genetic Material, Lymphoid Cells, T lymphocyte receptor complex, Transcriptome Profiles, Carcinomas, Taf[[II]]250, TCR, Tcr, Immunotherapies, TAF[[II]]230, Peripheral Blood, Adult Liver Cancers, Hepatocellular carcinoma, Hepatoma, p32, postnatal growth, expanded, Ex, Benign Neoplasms, TAF[II]250, FLO10, Cancers, CG17603, HERP, TAF[[II]], SmokTcr, Malignant Neoplasms, Reticuloendothelial System, l(2)01270, DmelCG17603, Taf250, Patient, enlarged, Material, SR3-5, Gene Expression Profiles, SNAP, RNA Sequence Analysis, PBMCs, Cells, Hepatocellular, Dominant negative form of Smok, l(2)ey, Cistron, T-cell receptor complex, CD8, Hepatocellular Carcinomas, Signature, other neoplasm, growth, Neoplasia, TAF230, TAF1, FLORAL DEFECTIVE 10"],"additional_accession":[]},"is_claimable":false,"name":"Peking University BIOPIC Data Access Committee (PUBDAC).The DATA ACCESS AGREEMENT is provided at https://github.com/zhangyybio/single-T-cell-data-access. Applicants can request access to the data by directly downloading it or by sending an email to cancerpku@pku.edu.cn. The process that is used to approve an application includes verifying the institution, participants and research purposes of the application. In general this process will take about two weeks. In principal, any academic research ","description":"Data Access Committee EGAC00001000551","dates":{"output":"2025-1-9"},"accession":"EGAC00001000551","cross_references":{"TAXONOMY":["9606"],"pubmed":["28622514"],"EGA":["EGAS00001002791","EGAS00001003883","EGAS00001003449","EGAS00001003973","EGAS00001002072","EGAS00001002430","EGAS00001003889","EGAD00001003910","EGAD00001005960","EGAD00001003337","EGAD00001004148","EGAD00001003999","EGAD00001005365","EGAD00001005448","EGAD00001004149","EGAD00001005961","EGAD00001005373"]}}