Observations on potential novel transcripts from RNA-Seq data

2011 ◽  
Vol 6 (2) ◽  
pp. 275-282 ◽  
Author(s):  
Chao Ye ◽  
Linxi Liu ◽  
Xi Wang ◽  
Xuegong Zhang
Keyword(s):  
Rna Seq ◽  
Novel Transcripts

Abstract 286: Long Noncoding RNAs Are Differentially Expressed in Heart Failure

2012 ◽  
Vol 111 (suppl_1) ◽  
Author(s):  
Emma L Robinson ◽  
Syed Haider ◽  
Hillary Hei ◽  
Richard T Lee ◽  
Roger S Foo
Keyword(s):  
Gene Expression ◽  
Heart Failure ◽  
Significant Proportion ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Control Of Gene Expression ◽  
Failing Heart ◽  
Novel Transcripts ◽  
Non Coding Rnas

Heart failure comprises of clinically distinct inciting causes but a consistent pattern of change in myocardial gene expression supports the hypothesis that unifying biochemical mechanisms underlie disease progression. The recent RNA-seq revolution has enabled whole transcriptome profiling, using deep-sequencing technologies. Up to 70% of the genome is now known to be transcribed into RNA, a significant proportion of which is long non-coding RNAs (lncRNAs), defined as polyribonucleotides of ≥200 nucleotides. This project aims to discover whether the myocardium expression of lncRNAs changes in the failing heart. Paired end RNA-seq from a 300-400bp library of ‘stretched’ mouse myocyte total RNA was carried out to generate 76-mer sequence reads. Mechanically stretching myocytes with equibiaxial stretch apparatus mimics pathological hypertrophy in the heart. Transcripts were assembled and aligned to reference genome mm9 (UCSC), abundance determined and differential expression of novel transcripts and alternative splice variants were compared with that of control (non-stretched) mouse myocytes. Five novel transcripts have been identified in our RNA-seq that are differentially expressed in stretched myocytes compared with non-stretched. These are regions of the genome that are currently unannotated and potentially are transcribed into non-coding RNAs. Roles of known lncRNAs include control of gene expression, either by direct interaction with complementary regions of the genome or association with chromatin remodelling complexes which act on the epigenome.Changes in expression of genes which contribute to the deterioration of the failing heart could be due to the actions of these novel lncRNAs, immediately suggesting a target for new pharmaceuticals. Changes in the expression of these novel transcripts will be validated in a larger sample size of stretched myocytes vs non-stretched myocytes as well as in the hearts of transverse aortic constriction (TAC) mice vs Sham (surgical procedure without the aortic banding). In vivo investigations will then be carried out, using siLNA antisense technology to silence novel lncRNAs in mice.

The identification and characterization of novel transcripts from RNA-seq data

2015 ◽  
Vol 17 (4) ◽  
pp. 678-685 ◽  
Author(s):  
Tyler Weirick ◽  
Giuseppe Militello ◽  
Raphael Müller ◽  
David John ◽  
Stefanie Dimmeler ◽  
...  
Keyword(s):  
Rna Seq ◽  
Novel Transcripts ◽  
Identification And Characterization

scholarly journals A long-read RNA-seq approach to identify novel transcripts of very large genes

2020 ◽  
Vol 30 (6) ◽  
pp. 885-897
Author(s):  
Prech Uapinyoying ◽  
Jeremy Goecks ◽  
Susan M. Knoblach ◽  
Karuna Panchapakesan ◽  
Carsten G. Bonnemann ◽  
...  
Keyword(s):  
Rna Seq ◽  
Long Read ◽  
Novel Transcripts ◽  
Large Genes

scholarly journals Micro-dissection and integration of long and short reads to create a robust catalog of kidney compartment-specific isoforms

2021 ◽  
Author(s):  
Ridvan Eksi ◽  
Daiyao Yi ◽  
Hongyang Li ◽  
Bradley Godfrey ◽  
Lisa R. Mathew ◽  
...  
Keyword(s):  
Human Kidney ◽  
Computational Pipeline ◽  
Rna Seq ◽  
Healthy Human ◽  
Short Reads ◽  
Short Read Sequencing ◽  
Pacbio Rs Ii ◽  
Long Reads ◽  
Novel Transcripts ◽  
Isoform Expression

AbstractStudying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-insterstitial compartments carry out drastically different physiological functions and thus presumably their isoform expression also differs. We aim at developing an experimental and computational pipeline for identifying isoforms at microscopic structure-level. We microdissed glomerular and tubulo-interstitial compartments from healthy human kidney tissues from two cohorts. The two compartments were separately sequenced with the PacBio RS II platform. These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. We identified 14,739 and 14,259 annotated transcripts, and 17,268 and 13,118 potentially novel transcripts in the glomerular and tubulo-interstitial compartments, respectively. Of note, relying solely on either short or long reads would have resulted in many erroneous identifications. We identified distinct pathways involved in glomerular and tubulointerstitial compartments at the isoform level.We demonstrated the possibility of micro-dissecting a tissue, incorporating both long- and short-read sequencing to identify isoforms for each compartment.

scholarly journals RNAtor: an Android-based application for biologists to plan RNA sequencing experiments

2016 ◽  
Author(s):  
Shruti Kane ◽  
Himanshu Garg ◽  
Neeraja M. Krishnan ◽  
Aditya Singh ◽  
Binay Panda
Keyword(s):  
Rna Sequencing ◽  
Mobile Applications ◽  
Mobile Application ◽  
Splice Variants ◽  
Real Data ◽  
Flow Cell ◽  
Rna Seq ◽  
Amount Of Information ◽  
Novel Transcripts ◽  
Google Play

AbstractRNA sequencing (RNA-seq) is a powerful technology for identification of novel transcripts (coding, non-coding and splice variants), understanding of transcript structures and estimation of gene and/or allelic expression. There are specific challenges that biologists face in determining the number of replicates to use, total number of sequencing reads to generate for detecting marginally differentially expressed transcripts and the number of lanes in a sequencing flow cell to use for the production of right amount of information. Although past studies attempted answering some of these questions, there is a lack of accessible and biologist-friendly mobile applications to answer these questions. Keeping this in mind, we have developed RNAtor, a mobile application for Android platforms, to aid biologists in correctly designing their RNA-seq experiments. The recommendations from RNAtor are based on simulations and real data.Availability and ImplementationThe Android version of RNAtor is available on Google Play Store and the code from GitHub (https://github.com/binaypanda/RNAtor).

scholarly journals Transcriptomic analysis of cadmium stressed Tamarix hispida revealed novel transcripts and the importance of ABA network

2021 ◽  
Author(s):  
Caiqiu Gao ◽  
Pei-Long Wang ◽  
Xiao-Jin Lei ◽  
Yuan-Yuan Wang ◽  
Bai-chao Liu ◽  
...  
Keyword(s):  
Environmental Problem ◽  
Salt Content ◽  
Tamarix Hispida ◽  
Rna Seq ◽  
Cd Stress ◽  
Ros Metabolism ◽  
Hormone Responses ◽  
Novel Transcripts ◽  
Stress Sensing ◽  
Transcriptomic Changes

Abstract Aim Cadmium (Cd) pollution is widely detected in soil and has been recognized as a major environmental problem. Tamarix hispida is a woody halophyte, which can form natural forest on desert and the soil with 0.5–1% salt content, making it an ideal plant for research investigating the effects of various stresses on plants. However, no systematic study has investigated the molecular mechanism of Cd tolerance in T. hispida.Methods In this study, the RNA-seq technique was applied to analyze the transcriptomic changes in T. hispida treated with 150 µmol L− 1 CdCl2 for 24, 48 and 72 h compared with control.Results In total, 72764 unigenes exhibited similar sequences in the NR database, while 41528 unigenes (36.3% of all the unigenes) did not exhibit similar sequences, which may be new transcripts. In addition, 6778, 8282 and 8601 DEGs were detected at 24, 48 and 72 h, respectively. Functional annotation analysis indicated that many genes may be involved in several aspects of the Cd stress response, including ion bonding, signal transduction, stress sensing, hormone responses and ROS metabolism. A ThUGT gene from the abscisic acid (ABA) signaling pathway can enhance the Cd resistance ability of T. hispida by regulating the production of reactive oxygen species under Cd stress and inhibiting T. hispida absorption of Cd.Conclusion The new transcriptome resources and data that we present in this study for T. hispida may substantially facilitate molecular studies of the mechanisms governing Cd resistance.

scholarly journals Comprehensive assembly of novel transcripts from unmapped human RNA‐Seq data and their association with cancer

2015 ◽  
Vol 11 (8) ◽  
pp. 826 ◽  
Author(s):  
Majid Kazemian ◽  
Min Ren ◽  
Jian‐Xin Lin ◽  
Wei Liao ◽  
Rosanne Spolski ◽  
...  
Keyword(s):  
Rna Seq ◽  
Novel Transcripts

scholarly journals Identification of novel transcripts in annotated genomes using RNA-Seq

2011 ◽  
Vol 27 (17) ◽  
pp. 2325-2329 ◽  
Author(s):  
A. Roberts ◽  
H. Pimentel ◽  
C. Trapnell ◽  
L. Pachter
Keyword(s):  
Rna Seq ◽  
Novel Transcripts

scholarly journals AuPairWise: a method to estimate RNA-seq replicability through co-expression

2016 ◽  
Author(s):  
Sara Ballouz ◽  
Jesse Gillis
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Ad Hoc ◽  
Dynamic Range ◽  
Control Measures ◽  
Rna Seq ◽  
Distribution Of Values ◽  
Gene Level ◽  
Novel Transcripts ◽  
Gene Expression Levels

In addition to detecting novel transcripts and higher dynamic range, a principal claim for RNA-sequencing has been greater replicability, typically measured in sample-sample correlations of gene expression levels. Through a re-analysis of ENCODE data, we show that replicability of transcript abundances will provide misleading estimates of the replicability of conditional variation in transcript abundances (i.e., most expression experiments). Heuristics which implicitly address this problem have emerged in quality control measures to obtain 'good' differential expression results. However, these methods involve strict filters such as discarding low expressing genes or using technical replicates to remove discordant transcripts, and are costly or simply ad hoc. As an alternative, we model gene-level replicability of differential activity using co-expressing genes. We find that sets of housekeeping interactions provide a sensitive means of estimating the replicability of expression changes, where the co-expressing pair can be regarded as pseudo-replicates of one another. We model the effects of noise that perturbs a gene's expression within its usual distribution of values and show that perturbing expression by only 5% within that range is readily detectable (AUROC~0.73). We have made our method available as a set of easily implemented R scripts.

scholarly journals RNAtor: an Android-based application for biologists to plan RNA sequencing experiments

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 997
Author(s):  
Shruti Kane ◽  
Himanshu Garg ◽  
Neeraja M. Krishnan ◽  
Aditya Singh ◽  
Binay Panda
Keyword(s):  
Rna Sequencing ◽  
Mobile Applications ◽  
Mobile Application ◽  
Splice Variants ◽  
Real Data ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Sample Analysis ◽  
Allele Expression ◽  
Novel Transcripts

RNA sequencing (RNA-seq) is a powerful technology that allows one to assess the RNA levels in a sample. Analysis of these levels can help in identifying novel transcripts (coding, non-coding and splice variants), understanding transcript structures, and estimating gene/allele expression. Biologists face specific challenges while designing RNA-seq experiments. The nature of these challenges lies in determining the total number of sequenced reads and technical replicates required for detecting marginally differentially expressed transcripts. Despite previous attempts to address these challenges, easily-accessible and biologist-friendly mobile applications do not exist. Thus, we developed RNAtor, a mobile application for Android platforms, to aid biologists in correctly designing their RNA-seq experiments. The recommendations from RNAtor are based on simulations and real data.

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