scholarly journals High-Throughput Transcriptome Sequencing for Snp and Gene Discovery in a Moth

2012 ◽  
Vol 41 (4) ◽  
pp. 997-1007 ◽  
Author(s):  
Nicholas J. Miller ◽  
Jing Sun ◽  
Thomas W. Sappington
Keyword(s):  
High Throughput ◽  
Transcriptome Sequencing ◽  
Gene Discovery

scholarly journals Organoid Models for Cancer Research

2019 ◽  
Vol 3 (1) ◽  
pp. 223-234 ◽  
Author(s):  
Hans Clevers ◽  
David A. Tuveson
Keyword(s):  
Cancer Research ◽  
Tumor Microenvironment ◽  
Personalized Medicine ◽  
High Throughput ◽  
Stromal Cells ◽  
Transcriptome Sequencing ◽  
Cancer Biology ◽  
Three Dimensional ◽  
Model Systems ◽  
Liver Cancers

Organoid cultures have emerged as powerful model systems accelerating discoveries in cellular and cancer biology. These three-dimensional cultures are amenable to diverse techniques, including high-throughput genome and transcriptome sequencing, as well as genetic and biochemical perturbation, making these models well suited to answer a variety of questions. Recently, organoids have been generated from diverse human cancers, including breast, colon, pancreas, prostate, bladder, and liver cancers, and studies involving these models are expanding our knowledge of the etiology and characteristics of these malignancies. Co-cultures of cancer organoids with non-neoplastic stromal cells enable investigation of the tumor microenvironment. In addition, recent studies have established that organoids have a place in personalized medicine approaches. Here, we describe the application of organoid technology to cancer discovery and treatment.

scholarly journals Gene discovery and annotation using LCM-454 transcriptome sequencing

2006 ◽  
Vol 17 (1) ◽  
pp. 69-73 ◽  
Author(s):  
S. J. Emrich ◽  
W. B. Barbazuk ◽  
L. Li ◽  
P. S. Schnable
Keyword(s):  
Transcriptome Sequencing ◽  
Gene Discovery ◽  
454 Transcriptome Sequencing

scholarly journals High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Yue Him Wong ◽  
Jin Sun ◽  
Li Sheng He ◽  
Lian Guo Chen ◽  
Jian-Wen Qiu ◽  
...  
Keyword(s):  
High Throughput ◽  
Transcriptome Sequencing ◽  
Cold Seep

scholarly journals A Pan-Cancer Analysis of Alternative Splicing Events Reveals Novel Tumor-Associated Splice Variants of Matriptase

2014 ◽  
Vol 13 ◽  
pp. CIN.S19435 ◽  
Author(s):  
Daryanaz Dargahi ◽  
Richard D. Swayze ◽  
Leanna Yee ◽  
Peter J. Bergqvist ◽  
Bradley J. Hedberg ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
High Throughput ◽  
Messenger Rna ◽  
Transcriptome Sequencing ◽  
Splice Variants ◽  
Flow Cytometric Analysis ◽  
Chinese Hamster ◽  
Lung Squamous Cell Carcinoma ◽  
The Cancer Genome Atlas ◽  
Sequencing Data

High-throughput transcriptome sequencing allows identification of cancer-related changes that occur at the stages of transcription, pre-messenger RNA (mRNA), and splicing. In the current study, we devised a pipeline to predict novel alternative splicing (AS) variants from high-throughput transcriptome sequencing data and applied it to large sets of tumor transcriptomes from The Cancer Genome Atlas (TCGA). We identified two novel tumor-associated splice variants of matriptase, a known cancer-associated gene, in the transcriptome data from epithelial-derived tumors but not normal tissue. Most notably, these variants were found in 69% of lung squamous cell carcinoma (LUSC) samples studied. We confirmed the expression of matriptase AS transcripts using quantitative reverse transcription PCR (qRT-PCR) in an orthogonal panel of tumor tissues and cell lines. Furthermore, flow cytometric analysis confirmed surface expression of matriptase splice variants in chinese hamster ovary (CHO) cells transiently transfected with cDNA encoding the novel transcripts. Our findings further implicate matriptase in contributing to oncogenic processes and suggest potential novel therapeutic uses for matriptase splice variants.

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