RNA-seq-based transcriptome profiling reveals differential gene expression in the lungs of Sprague–Dawley rats during early-phase acute hypobaric hypoxia

2015 ◽  
Vol 290 (6) ◽  
pp. 2225-2240 ◽  
Author(s):  
Priyanka Sharma ◽  
Anju Bansal ◽  
Prakash Chand Sharma
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Early Phase ◽  
Hypobaric Hypoxia ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Sprague Dawley ◽  
Acute Hypobaric Hypoxia ◽  
Sprague Dawley Rats ◽  
Differential Gene

scholarly journals Comparative Neuronutritive Protection of Citrus sinensis & Vitamin C on Differential Gene Expression in Brain Tissues of Female Sprague Dawley Rats

2012 ◽  
Vol 26 (S1) ◽  
Author(s):  
Olorunwa Olufunmilayo Ogunleye ◽  
Ayorinde Babatunde James ◽  
Osaretin Albert Ebuehi ◽  
Bamidele Iwalokun ◽  
Gbemisola Morounke Saibu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin C ◽  
Differential Gene Expression ◽  
Citrus Sinensis ◽  
Sprague Dawley ◽  
Sprague Dawley Rats ◽  
Differential Gene ◽  
Brain Tissues

scholarly journals Evaluating Methods for Differential Gene Expression And Alternative Splicing Using Internal Synthetic Controls

2020 ◽  
Author(s):  
Sudeep Mehrotra ◽  
Revital Bronstein ◽  
Daniel Navarro-Gomez ◽  
Ayellet V. Segrè ◽  
Eric A. Pierce
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Differential Gene Expression ◽  
Internal Control ◽  
Accurate Determination ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Specificity And Sensitivity ◽  
Differential Gene ◽  
Synthetic Controls

AbstractHigh-throughput transcriptome sequencing has become a powerful tool in the study of human diseases. Identification of causal mechanisms may entail analysis of differential gene expression (DGE), differential transcript/isoform expression (DTE) and identification, classification and quantification of alternative splicing (AS) and/or detection of novel AS events. For such a global transcriptome profiling execution of multi-level data analysis methodologies is required. Each level presents its own unique challenges and the questions about their performance remains. In this work we present results from systematic and consistent assessing and comparing a number of widely used methods for detecting DGE, DTE and AS using internal control “spike-in” sequences (Sequins) in RNA-seq data. We demonstrated that inclusion of internal controls in RNA-seq experiments allows accurate determination of lower bounds detection levels, and better assessment of DGE, DTE and AS accuracy and sensitivity. Tools for RNA-seq read alignment and detection of DGE performed reasonably. More efforts are needed to improve specificity and sensitivity of DTE and AS detection. Low expression of isoforms accompanied with sequencing depth does impact sensitivity and specificity of DTE and AS tools.

scholarly journals Differential Gene Expression by RNA-Seq Analysis of the Primo Vessel in the Rabbit Lymph

2019 ◽  
Vol 12 (1) ◽  
pp. 11-19 ◽  
Author(s):  
Jun-Young Shin ◽  
Sang-Heon Choi ◽  
Da-Woon Choi ◽  
Ye-Jin An ◽  
Jae-Hyuk Seo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Rna Seq ◽  
Differential Gene

scholarly journals Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

2013 ◽  
Vol 14 (9) ◽  
pp. R95 ◽  
Author(s):  
Franck Rapaport ◽  
Raya Khanin ◽  
Yupu Liang ◽  
Mono Pirun ◽  
Azra Krek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Comprehensive Evaluation ◽  
Rna Seq ◽  
Differential Gene Expression Analysis ◽  
Analysis Methods ◽  
Differential Gene
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