Accession PRJCA001228
Title A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
Relevance Medical
Data Types Transcriptome or Gene expression
Organisms Homo sapiens
Description Esophageal squamous cell carcinomas (ESCC) is a leading cause of cancer death, especially in eastern Asian area. Mapping the transcriptional landscape such as isoforms, fusion transcripts as well as long noncoding RNAs, have played a central role to understand the regulating mechanism during malignant processes. However, canonical methods such as microarrays and short-read RNA-seq are difficult to define the entire polyadenylated RNA molecule structure. Here we use PacBio SMRT platform to generate high-quality long reads, and to survey the full length RNA molecules in five esophageal squamous cell lines. Compared with the recent annotations of human transcriptome (Ensemble 38 release 91), SMRT data reveal many unannotated transcripts and isoform structures in each cell line, indicating the diverse alternative splicing patterns and transcribed RNA molecules. Based on SMRT long reads, many lncRNAs are also predicted with high confidence by multiple analyzing tools. Utilizing vigorous heuristics criteria, we also detect multiple transcript fusions, which are not documented in current gene fusion database or readily identified from RNA-seq short reads. Overall, our study provides a global view of the full length transcriptome with long-read single molecule sequencing, and elucidates a more comprehensive assessment of the true complexity in esophageal cells.
Sample scope Multiisolate
Release date 2019-07-10
Grants
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) 81673037
National Natural Science Foundation of China (NSFC) 81472613
National Natural Science Foundation of China (NSFC) 81772532
Submitter Jianzhen    Xu  (jzxu01@stu.edu.cn)
Organization Shantou University Medical College
Submission date 2019-01-19

Project Data

Resource name Description
BioSample (5) -
SAMC055208 A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
SAMC055207 A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
SAMC055206 A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
SAMC055205 A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
SAMC055204 A survey of the transcriptional landscape in esophageal squamous cells with long read single molecule real-time sequencing
GSA (1) -
CRA001374 PacBio data for Shantou University Medical College
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