T cell subsets in lung cancer and feature genes thereof
A gene and cell technology, applied in the field of identification, characterization and enrichment of T cell subsets, can solve problems such as categories, differentiation and inhibited pathways are not fully understood
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Embodiment 1
[0201] Example 1 Acquisition of single-cell transcriptome data of T cells
[0202] 1. Clinical sample collection
[0203] Surgical tissue and peripheral blood, including cancer tissue and adjacent normal tissue, were collected from Peking University Cancer Hospital and Peking University Third Hospital, and peripheral blood (3ml) was collected. Patients with non-small cell lung cancer, including squamous cell carcinoma and adenocarcinoma, did not receive preoperative adjuvant radiotherapy or chemotherapy, a total of 9 cases. This study complied with the medical ethics standards of the Declaration of Helsinki and was approved by the Medical Ethics Committee of Peking University.
[0204] Blood samples were collected in EDTA anticoagulant tubes and temporarily stored on ice before surgery; cancer tissue and adjacent normal tissue samples were collected during the operation, and necrotic tissue was removed from the cancer tissue; adjacent normal tissue was normal tissue at least ...
Embodiment 2
[0259] Embodiment 2 biological information analysis
[0260] 1. Data comparison and quality control
[0261] For the reads (reads) obtained from the sequencer, the low-quality parts are first removed, and the retention criteria are as follows: ① unknown bases cannot exceed 10% of the total sequence of a given read, ② bases with a quality value lower than 5 cannot More than 50%, ③ cannot contain linker sequences. Use GSNAP software to complete the alignment, the human genome reference sequence version is hg19, and the parameter selection --novelsplicing 1-n 10-i 1-M 2. When calculating gene expression, the reference gene set used is from UCSC's "knownGene.txt", and the R language package "findOverlaps" is used to count the attribution of reads on the gene, and the TPM value is used to calibrate the expression of each gene in each cell amount, the formula used is:
[0262] where C ij Expressed as the number of reads for gene i in cell j.
[0263] T cells with low data vol...
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