Prediction of new long non-coding RNA of laryngeal carcinoma by high-throughput RNA-Seq data
10.3760/cma.j.issn.1673-0860.2014.08.005
- VernacularTitle:利用高通量转录组测序数据预测喉鳞状细胞癌转录组新长链非编码RNA的初步研究
- Author:
Yang ZHANG
1
;
Guiming LIU
;
Guoliang WANG
;
Qi ZHONG
;
Xiaohong CHEN
;
Jugao FANG
;
Zhigang HUANG
Author Information
1. 耳鼻咽喉头颈科学教育部重点实验室(首都医科大学)
- Keywords:
Laryngeal neoplasms;
Carcinoma,squamous cell;
Transcriptome;
RNA,long noncoding;
Gene expression profiling;
Computation biology
- From:
Chinese Journal of Otorhinolaryngology Head and Neck Surgery
2014;49(8):637-642
- CountryChina
- Language:Chinese
-
Abstract:
Objective To screen and identify the new long non-coding RNAs from transcriptome of laryngeal squamous cell cancer using strand-specific RNA-Seq technology and bioinformatics tools,and to analyze the difference expression of these LncRNAs.Methods RNA was extracted from laryngeal squamous cell cancer tissues of 10 patients and the strand-specific libraries were constructed for high-throughput sequencing.The low-quality data were filtered and the high quality sequencing reads were mapped to the reference genome and assembled.The obtained transcripts were classified and annotated,the optimized LncRNA identification pipeline was used to discover novel LncRNA in these transcriptome,and the characteristics of LncRNA were analyzed.Results A more optimized pipeline were established and 134 new LncRNA transcripts were found,which was not included in the public database.The new LncRNA transcripts had some characteristics in length distribution,ORF length,and expression.Conclusion Some new LncRNA from the transcriptome of laryngeal carcinoma were identified,with different expression,and they may play an important role in laryngeal squamous cell cancer.
