scholarly journals SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis

2017 ◽  
Vol 3 (4) ◽  
pp. 186
Author(s):  
Redi Aditama ◽  
Zulfikar Achmad Tanjung ◽  
Widyartini Made Sudania ◽  
Toni Liwang
Keyword(s):  
Gene Expression ◽  
Large Scale ◽  
Analysis Tool ◽  
Rna Seq ◽  
Expression Studies ◽  
Galaxy Server ◽  
Local Facility ◽  
Computational Workflow ◽  
Gene Expression Studies ◽  
Next Generation Sequencing Ngs

<p class="Els-Abstract-text">RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.</p><p><strong>Keywords:</strong> FPKM; Galaxy workflow; Gene expression; RNA sequencing.</p>

scholarly journals A comprehensive rat transcriptome built from large scale RNA-seq-based annotation

2020 ◽  
Vol 48 (15) ◽  
pp. 8320-8331
Author(s):  
Xiangjun Ji ◽  
Peng Li ◽  
James C Fuscoe ◽  
Geng Chen ◽  
Wenzhong Xiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Significant Influence ◽  
Large Scale ◽  
Expression Patterns ◽  
Model Organism ◽  
Rna Seq ◽  
Disease Mechanisms ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Different Tissues

Abstract The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.

scholarly journals Finding the active genes in deep RNA-seq gene expression studies

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 778 ◽  
Author(s):  
Traver Hart ◽  
H Komori ◽  
Sarah LaMere ◽  
Katie Podshivalova ◽  
Daniel R Salomon
Keyword(s):  
Gene Expression ◽  
Rna Seq ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Active Genes

scholarly journals Trisomy 21 and Down syndrome: a short review

2008 ◽  
Vol 68 (2) ◽  
pp. 447-452 ◽  
Author(s):  
CA. Sommer ◽  
F. Henrique-Silva
Keyword(s):  
Gene Expression ◽  
Down Syndrome ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Short Review ◽  
Complex Disorder ◽  
Expression Studies ◽  
Gene Expression Studies ◽  
Chromosome Segments

Even though the molecular mechanisms underlying the Down syndrome (DS) phenotypes remain obscure, the characterization of the genes and conserved non-genic sequences of HSA21 together with large-scale gene expression studies in DS tissues are enhancing our understanding of this complex disorder. Also, mouse models of DS provide invaluable tools to correlate genes or chromosome segments to specific phenotypes. Here we discuss the possible contribution of HSA21 genes to DS and data from global gene expression studies of trisomic samples.

scholarly journals Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Robert Ekblom ◽  
Jon Slate ◽  
Gavin J. Horsburgh ◽  
Tim Birkhead ◽  
Terry Burke
Keyword(s):  
Gene Expression ◽  
454 Sequencing ◽  
Cdna Libraries ◽  
Small Scale ◽  
Rna Seq ◽  
Quantitative Gene Expression ◽  
Expression Studies ◽  
Number Of Genes ◽  
Gene Expression Studies ◽  
Generation Sequencing

Next-generation sequencing of transcriptomes (RNA-Seq) is being used increasingly in studies of nonmodel organisms. Here, we evaluate the effectiveness of normalising cDNA libraries prior to sequencing in a small-scale study of the zebra finch. We find that assemblies produced from normalised libraries had a larger number of contigs but used fewer reads compared to unnormalised libraries. Considerably more genes were also detected using the contigs produced from normalised cDNA, and microsatellite discovery was up to 73% more efficient in these. There was a positive correlation between the detected expression level of genes in normalised and unnormalised cDNA, and there was no difference in the number of genes identified as being differentially expressed between blood and spleen for the normalised and unnormalised libraries. We conclude that normalised cDNA libraries are preferable for many applications of RNA-Seq and that these can also be used in quantitative gene expression studies.

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