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
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