{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001004149"],"sample_count":["10"],"description":["EGA dataset EGAD00001004149"],"repository":["EGA"],"title":["bulk Exome-seq of the 5 HCC patients which also have the single cell T cell RNA-seq data"],"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, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, 2018., ENA/VASP"],"description_synonyms":["HYCC1, whole exome, Carcinoma, RNA, Ribonucleic, dTAF[[II]]230, TAF[[II]]250, d230, Liver, ribose nucleic acid, ribonucleic acids, number, TAF200, Cell Carcinoma, l(3)84Ab, dTAFII250, Liver Cell, RNS, adult hepatoma, BG:DS00004.13, TAFII-250, Hepatomas, TAF250/230, EfW1, Liver Cell Carcinoma, Client, presence, Cell, dTAF230, Cell Carcinomas, dmTAF[[II]]230, count in organism, TAFII250, HCC, Liver Cell Carcinomas, dmTAF1, Taf230, p230, yeast nucleic acid, Ribonukleinsaeure, Gene Products, Adult Liver Cancer, TAF[[II]]250/230, TFIID, pentosenucleic acids, Ribonucleic acids, Adult Liver, Non Polyadenylated, RNA Gene Products, TAF250, Carcinomas, Taf[[II]]250, ribonucleic acid, Acid, Taf200, DRCTNNB1A, dTAF[[II]]250, TAF[[II]]230, Adult Liver Cancers, Hepatocellular carcinoma, TFIID TAF250, Liver Cancer, Hepatoma, cel, cell, Non Polyadenylated RNA, Exomes, Non-Polyadenylated, adult primary hepatocellular carcinoma, Liver Cancers, HLD5, Taf1p, TAF[II]250, Cancers, Ribonucleic Acid, Dietary Fiber, Adult, CG17603, TAF[[II]], cardinality., Hepatocellular Carcinoma, Non-Polyadenylated RNA, dTAF250, DmelCG17603, Taf250, Patient, SR3-5, Clients, Hepatocellular, Hepatocellular Carcinomas, TAF, TAF230, Cancer, TAF1"],"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":["functions, Materials, single-organism developmental process, RNA Sequence Determination, Developmental Finding, Sequence Determination, FON1, Feature, Blood, postnatal development, clinical data, RNA Sequence, Activated, Gene Expression Profile, Nurture, growth and development, adult hepatoma, Profiles, Tumor, FLORAL ORGAN NUMBER 1, Hepatomas, Liver Cell Carcinoma, brl, dmTAF[[II]]230, Readability, SUP, CG9063, Activate, Analysis, domain, IKKg, KEY, Key, average, Transcriptional, Protein Motif, Project ENABLE, DRCTNNB1A, TFIID TAF250, Analyses, Identification, cel, Determination, Molecular, Tissue, Bdr, adult primary hepatocellular carcinoma, HLD5, Adult, Super protein, Sequence Determinations, BcDNA:GH03694, Based, Signatures, sp, SNAP-25, Hepatocellular Carcinoma, Gene Transcription, Maturation, Daily Living, Expression Signature, Transcriptomes, Malignancies, Lymphoid, DmelCG9063, Protein Domain, Tumors, Protein Feature, Carcinoma, Daily Living Function, dTAF[[II]]230, Liver, Array Feature, Expression Profiles, TAF200, Liver Cell, TAFII-250, TAF250/230, Exhausted, Determinations, Expanded, Gene Expression, DmIKKgamma, TAFII250, Signed, Benign, HCC, dIKK, 1270, Expression Signatures, Kenny, GENA70, Genetic Materials, Lymphoid Cell, Educate, Adult Liver, DNA Sequence, Region, Expression Profile, Domain, Genetic Material, Clinical Data, Transcriptome Profiles, Carcinomas, Developmental, Image Feature, Delineated, Immunotherapies, Delineation, Hepatoma, p32, BcDNAGH03694, IKK-gamma, Delineate, expanded, Ex, Benign Neoplasms, Coupled, CG17603, Features, TAF[[II]], 3L6, SmokTcr, Malignant Neoplasms, Identified, Health, DmelCG16910, Taf250, Patient, enlarged, rich, Imaging Feature, Material, SR3-5, PBMCs, Cells, Base, Dominant negative form of Smok, l(2)ey, functioning, Cistron, T-cell receptor complex, Hepatocellular Carcinomas, other neoplasm, TAF230, Nucleotide Sequence, FLORAL DEFECTIVE 10, HYCC1, big, transcription, Understanding., Clinical Batch, d230, Health Resource, Transcriptome Profile, Neoplasms, How Exhausted at Present, infiltrating, Benign Neoplasm, How True Feel Exhausted Right Now, Cell Carcinoma, Gene, dTAFII250, Isolated, SUPERMAN, Development, Malignant, EfW1, dIKK-gamma, Cell Carcinomas, Responder protein Smok-Tcr, large, DmelCG4114, dmTAF1, isolation, Liver Cell Carcinomas, Taf230, DmIKK-gamma, PBMC, Adult Liver Cancer, dmIKKgamma, IKK[[gamma]], MAL, Resources, TAF250, Taf200, Transcription, RNA Expression, Routine Signature, dTAF[[II]]250, Couple, Clinical, Genetic, Malignancy, Liver Cancer, Activation, cell, Profile, Liver Cancers, Genetic Transcription, Taf1p, Coupling, Sequencing, Neoplasias, dTAF250, Mif1, PERFORMED, IKK, RNA Sequence Analyses, Clients, great, RNA Sequencing, Characteristics, TAF, Lymphocyte, Cancer, Sequence Analyses, Perform, SINGLE, RNA, TAF[[II]]250, Transcriptome, Malignant Neoplasm, whole blood, RNA Sequence Determinations, T-lymphocyte receptor complex, CG4114, Leu2, l(3)84Ab, BG:DS00004.13, Synaptosomal-associated 25 kDa protein, Cistrons, Client, Cell, dTAF230, development, Sequences, IKKgamma, 2.7.11.1, Characteristic, Clinical Lot, TCR complex, Resource, Sequence, ENABLE, p230, Gene Expression Signatures, Neoplasm, TAF[[II]]250/230, clinical, TFIID, Gene Expression Signature, activate, Lymphoid Cells, T lymphocyte receptor complex, Performed, signatureText, Taf[[II]]250, Basic, TCR, Tcr, Single Person, TAF[[II]]230, Peripheral Blood, Adult Liver Cancers, Hepatocellular carcinoma, Dmikkgamma, postnatal growth, Basis, TAF[II]250, FLO10, Cancers, CG16910, HERP, Reticuloendothelial System, Adjacent, Specified, l(2)01270, Protein Region, DmelCG17603, Only, Specific, Gene Expression Profiles, SNAP, RNA Sequence Analysis, Hepatocellular, Solitary, Single, CD8, Signature, Isolation, growth, Neoplasia, Alone, Advise Before Life Ends, Motif, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-BIOPIC-06-06-2018-15:55:49:835-165 - samples","description":"bulk Exome-seq data of the 5 HCC patinets. Single cell RNA seq data of these patients was under the accession number EGAD00001003337","dates":{"updated":"2018-06-11 16:51:02"},"accession":"EGAD00001004149","cross_references":{"TAXONOMY":["9606"],"pubmed":["28622514"],"EGA":["EGAC00001000551","EGAS00001002072"]}}