A method for mining key RNA functions based on high-throughput experimental data mining
An experimental data, high-throughput technology, applied in the field of bioinformatics, can solve problems such as unavailability of applications, incomplete open data sets, lack of databases to help reveal functional mechanisms, etc., to achieve the effect of increasing the sample size
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Embodiment 1
[0124] 1) Sample collection: 100 patients with lung adenocarcinoma whose pathology has been clinically diagnosed and whose paraffin tissue can be obtained were selected as the research objects. Based on the high-throughput transcriptome sequencing (RNA-seq) method, the tissue samples (cancerous and paracancerous, a total of 200 samples) were subjected to transcriptome sequencing and bioinformatics analysis. The research subjects were all selected from Table 1 of Thoracic Cancer 9 (2018) 1680-1686, and the sample screening requirements were as follows: lung adenocarcinoma, confirmed information, and complete clinical follow-up information.
[0125] 2) RNA sequencing data preprocessing: use the fastx_clipper tool in fastx_toolkit to remove sequencing adapters, use the fastq_quality_filter tool in fastx_toolkit to remove low-quality sequencing reads, and then use tophat for data comparison. The reference genome is human hg19. In this way, the original sequencing reads of each sam...
Embodiment 2
[0131] 1) Sample collection: 10 patients with small cell lung cancer whose pathology has been clinically diagnosed and whose paraffin tissue can be obtained were selected as the research object. Tissue samples (lung cancer tissue and paracancerous tissue, a total of 20 samples) were tested based on the RNA high-throughput sequencing method. Sample screening requirements are as follows: small cell lung cancer, all patient specimens have been confirmed by the pathology department, the postoperative survival time is more than 3 months, and complete clinical follow-up information is available.
[0132] 2) Selection of accompanying data sets: Using public database resources, the RNA- Seq raw data, the data set number is gse60052, the download link is https: / / www.ncbi.nlm.nih.gov / sra? linkname=bioproject_sra_all&from_uid=257389, the clinical information of these samples is consistent with the clinical samples of this analysis, and can be combined for analysis.
[0133] 3) Data pre...
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