Method for annotating cell identities based on single cell transcriptome clustering results

A transcriptome and single-cell technology, applied in genomics, proteomics, instruments, etc.

Active Publication Date: 2019-07-26
广州序科码医学检验实验室有限公司
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  • Abstract
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  • Claims
  • Application Information

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  • Method for annotating cell identities based on single cell transcriptome clustering results
  • Method for annotating cell identities based on single cell transcriptome clustering results
  • Method for annotating cell identities based on single cell transcriptome clustering results

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Embodiment 1

[0036] An embodiment of the method for annotating cell identity based on single-cell transcriptome clustering results in the present invention includes the following steps:

[0037] 1) Library construction and sequencing

[0038] A case of fresh nasopharyngeal carcinoma tissue (male, 42 years old, pathologically diagnosed as poorly differentiated squamous cell carcinoma of the nasopharynx) was obtained from the Department of Otorhinolaryngology, Guangzhou Twelfth People's Hospital. Immediately put the cancer tissue into tissue culture medium, keep it on ice, and make cell suspension within two hours. After the cell counter detects that the proportion of viable cells exceeds 90%, it is sent to Guangzhou Sequoma Biotechnology Co., Ltd. for 10X genomics library construction. After the library is built, it will be sent to Beijing Annoroad Gene Technology Co., Ltd. for sequencing. The sequencing platform was Illumina Hiseq X, and the sequencing depth was packet lane sequencing. ...

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Abstract

The invention discloses a method for annotating cell identities based on single cell transcriptome clustering results. The method comprises the following steps: S1, providing survival cells, establishing a library by using 10X genetics, and sequencing to obtain transcriptome sequencing data; S2, filtering the sequencing data obtained in the step S1, then carrying out initial analysis by using thesoftware cellranger, and outputting original data; S3, analyzing the original data output in the step S2; S4, performing cell identity annotation, including the steps: S41, classifying the tag genes of the Cell Marker database according to cell types; S42, sorting the tag genes screened out by the FindAllMarkers function according to a P value; S43, taking an intersection of the tag gene of each type of cells in the Cell Marker database and a cell subset tag gene screened by the FindAllMarkers function, and scoring according to the intersection gene; and S44, sorting according to the score ofthe gene intersection, and annotating the cell type corresponding to the highest score as the cell identity of the current subgroup. By adopting the method for annotating cell identities based on single cell transcriptome clustering results disclosed by the invention, the cells can be accurately and quickly classified and subjected to identity annotation.

Description

technical field [0001] The invention relates to the technical field of cell classification, in particular to a method for annotating cell identity based on single-cell transcriptome clustering results. Background technique [0002] The 10X genomics sequencing platform is capable of simultaneously examining the transcriptomes of tens of thousands of single cells, so they can be clustered into different categories based on their gene expression profiles. The biggest challenge currently encountered is how to annotate the identities of these different classes of cells. Because there are hundreds of types of cells, we cannot fully grasp the signature genes expressed by each cell. The main purpose of 10X genomics sequencing is to discover new cell types. This poses a great challenge for us. [0003] 10x Genomics sequencing platform (workflow see figure 1 ) using a water-in-oil microreaction system, each oil droplet contains a single cell. Different oil droplets are added with...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/00G16B40/00
Inventor 黄仲曦章建平汪佳宏林献威潘星华
Owner 广州序科码医学检验实验室有限公司
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