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Series GSE98638 Query DataSets for GSE98638
Status Public on May 17, 2017
Title Landscape of infiltrating T cells in liver cancer revealed by single-cell sequencing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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 single T cells isolated from peripheral blood, tumor and adjacent normal tissues from hepatocellular carcinoma patients.
 
Overall design T cells from HCC patients were sorted, profiled by Smart-seq2 and Tang2010 protocol (for patient P1202, the suffix "t" indicate cells from this patient were processed using Tang2010 protocol; cells from other patients were processed using SMART-Seq2) and sequenced on Illumina HiSeq2500 and HiSeq4000. Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high) were sorted to perform RNA sequencing. The categories ("sampleType" column in the SAMPLES section) contain PTC(CD8+ T cells from peripheral blood), NTC(CD8+ T cells from adjacent normal liver tissues) ,TTC (CD8+ T cells from tumor), PTH(CD3+, CD4+ and CD25- T cells from peripheral blood), NTH(CD3+, CD4+ and CD25- T cells from adjacent normal liver tissues), TTH(CD3+, CD4+ and CD25- T cells from tumor), PTR(CD3+, CD4+ and CD25high T cells from peripheral blood), NTR(CD3+, CD4+ and CD25high T cells from adjacent normal liver tissues), TTR(CD3+, CD4+ and CD25high T cells from tumor), JTH(CD3+, CD4+ and CD25- T cells from joint area between the tumor and the adjacent normal tissue),JTR(CD3+, CD4+ and CD25high T cells from joint area between the tumor and the adjacent normal tissue), JTC(CD3+CD8+ T cells from joint area between the tumor and the adjacent normal tissue)
Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002072
 
Contributor(s) Zheng C, Zheng L, Yoo J, Guo H, Zhang Y, Guo X, Kang B, Hu R, Huang J, Zhang Q, Liu Z, Dong M, Hu X, Ouyang W, Peng J, Zhang Z
Citation(s) 28622514
Submission date May 08, 2017
Last update date Mar 20, 2019
Contact name zemin zhang
E-mail zeminz@yahoo.com
Organization name Peking University
Department BIOPIC
Lab Zhang Lab
Street address Yiheyuan Road
City Beijing
ZIP/Postal code 100871
Country China
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM2602294 P0205
GSM2602295 P0508
GSM2602296 P0322
Relations
BioProject PRJNA385799

Listing of Individual Cells header descriptions
UniqueCell_ID
Patient
majorCluster
sampleType

Data table
UniqueCell_ID Patient majorCluster sampleType
NTC148-0322 P0322 C01_CD8-LEF1 NTC
NTC69-0407 P0407 C01_CD8-LEF1 NTC
NTC81-0407 P0407 C01_CD8-LEF1 NTC
NTC96-0407 P0407 C01_CD8-LEF1 NTC
NTC2-55-0508 P0508 C01_CD8-LEF1 NTC
PTC03-0205 P0205 C01_CD8-LEF1 PTC
PTC114-0205 P0205 C01_CD8-LEF1 PTC
PTC119-0205 P0205 C01_CD8-LEF1 PTC
PTC128-0205 P0205 C01_CD8-LEF1 PTC
PTC130-0205 P0205 C01_CD8-LEF1 PTC
PTC131-0205 P0205 C01_CD8-LEF1 PTC
PTC132-0205 P0205 C01_CD8-LEF1 PTC
PTC133-0205 P0205 C01_CD8-LEF1 PTC
PTC135-0205 P0205 C01_CD8-LEF1 PTC
PTC137-0205 P0205 C01_CD8-LEF1 PTC
PTC138-0205 P0205 C01_CD8-LEF1 PTC
PTC139-0205 P0205 C01_CD8-LEF1 PTC
PTC140-0205 P0205 C01_CD8-LEF1 PTC
PTC143-0205 P0205 C01_CD8-LEF1 PTC
PTC147-0205 P0205 C01_CD8-LEF1 PTC

Total number of rows: 5063

Table truncated, full table size 168 Kbytes.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE98638_HCC.TCell.S4070.norm.centered.txt.gz 145.6 Mb (ftp)(http) TXT
GSE98638_HCC.TCell.S5063.TPM.txt.gz 158.4 Mb (ftp)(http) TXT
GSE98638_HCC.TCell.S5063.count.txt.gz 33.9 Mb (ftp)(http) TXT
GSE98638_gene.length.txt.gz 105.3 Kb (ftp)(http) TXT
Processed data is available on Series record
Raw data provided as supplementary file

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