Transcriptome Profiling of Micromelalopha troglodyta (Lepidoptera: Notodontidae) Larvae under Tannin Stress Using Solexa Sequencing Technology

2021 ◽  
Vol 56 (3) ◽  
Author(s):  
Kai Feng ◽  
Fang Tang ◽  
Yu Zhang ◽  
Meiling Nong
Keyword(s):  
Transcriptome Profiling ◽  
Solexa Sequencing ◽  
Sequencing Technology ◽  
Solexa Sequencing Technology

scholarly journals Transcriptome Profiling of Chironomus kiinensis under Phenol Stress Using Solexa Sequencing Technology

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e58914 ◽  
Author(s):  
Chuanwang Cao ◽  
Zhiying Wang ◽  
Changying Niu ◽  
Nicolas Desneux ◽  
Xiwu Gao
Keyword(s):  
Transcriptome Profiling ◽  
Solexa Sequencing ◽  
Sequencing Technology ◽  
Phenol Stress ◽  
Solexa Sequencing Technology

scholarly journals Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

2011 ◽  
Vol 56 (20) ◽  
pp. 2119-2130 ◽  
Author(s):  
Hui Yang ◽  
YunXiang Mao ◽  
FanNa Kong ◽  
GuanPin Yang ◽  
Fei Ma ◽  
...  
Keyword(s):  
Porphyra Yezoensis ◽  
Solexa Sequencing ◽  
Sequencing Technology ◽  
Solexa Sequencing Technology

scholarly journals Sequencing of Chloroplast Genome Using Whole Cellular DNA and Solexa Sequencing Technology

2012 ◽  
Vol 3 ◽  
Author(s):  
Jian Wu ◽  
Bo Liu ◽  
Feng Cheng ◽  
Nirala Ramchiary ◽  
Su Ryun Choi ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Solexa Sequencing ◽  
Sequencing Technology ◽  
Cellular Dna ◽  
Solexa Sequencing Technology

scholarly journals New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Éderson Akio Kido ◽  
José Ribamar Costa Ferreira Neto ◽  
Roberta Lane de Oliveira Silva ◽  
Valesca Pandolfi ◽  
Ana Carolina Ribeiro Guimarães ◽  
...  
Keyword(s):  
Drought Stress ◽  
Target Genes ◽  
Present Report ◽  
Transcriptome Profiling ◽  
Water Deficit Stress ◽  
New Genes ◽  
Drought Tolerant ◽  
Blastn Analysis ◽  
Root Tissues ◽  
Solexa Sequencing Technology

In the scope of the present work, four SuperSAGE libraries have been generated, using bulked root tissues from four drought-tolerant accessions as compared with four bulked sensitive genotypes, aiming to generate a panel of differentially expressed stress-responsive genes. Both groups were submitted to 24 hours of water deficit stress. The SuperSAGE libraries produced 8,787,315 tags (26 bp) that, after exclusion of singlets, allowed the identification of 205,975 unitags. Most relevant BlastN matches comprised 567,420 tags, regarding 75,404 unitags with 164,860 different ESTs. To optimize the annotation efficiency, the Gene Ontology (GO) categorization was carried out for 186,191 ESTs (BlastN against Uniprot-SwissProt), permitting the categorization of 118,208 ESTs (63.5%). In an attempt to elect a group of the best tags to be validated by RTqPCR, the GO categorization of the tag-related ESTs allowed thein silicoidentification of 213 upregulated unitags responding basically to abiotic stresses, from which 145 presented no hits after BlastN analysis, probably concerning new genes still uncovered in previous studies. The present report analyzes the sugarcane transcriptome under drought stress, using a combination of high-throughput transcriptome profiling by SuperSAGE with the Solexa sequencing technology, allowing the identification of potential target genes during the stress response.

scholarly journals Prospects for the use of third generation sequencers for quantitative profiling of transcriptome

2018 ◽  
Vol 1 (4) ◽  
pp. e00086
Author(s):  
S.P. Radko ◽  
L.K. Kurbatov ◽  
K.G. Ptitsyn ◽  
Y.Y. Kiseleva ◽  
E.A. Ponomarenko ◽  
...  
Keyword(s):  
Single Molecule ◽  
Transcriptome Profiling ◽  
Third Generation ◽  
Sequencing Technology ◽  
Single Molecule Sequencing ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Biotechnology Companies ◽  
Oxford Nanopore Technologies ◽  
Quantitative Profiling

Transcriptome profiling is widely employed to analyze transcriptome dynamics when studying various biological processes at the cell and tissue levels. Unlike the second generation sequencers, which sequence relatively short fragments of nucleic acids, the third generation DNA/RNA sequencers developed by biotechnology companies “PacBio” and “Oxford Nanopore Technologies” allow one to sequence transcripts as single molecules and may be considered as potential molecular counters capable to measure the number of copies of each transcript with high throughput, sensitivity, and specificity. In the present review, the features of single molecule sequencing technologies offered by “PacBio” and “Oxford Nanopore Technologies” are considered alongside with their utility for transcriptome analysis, including the analysis of transcript isoforms. The prospects and limitations of the single molecule sequencing technology in application to quantitative transcriptome profiling are also discussed.

Comparative Transcriptome Profiling of Disruptive Technology, Single- Molecule Direct RNA Sequencing

2020 ◽  
Vol 15 (2) ◽  
pp. 165-172
Author(s):  
Chaithra Pradeep ◽  
Dharam Nandan ◽  
Arya A. Das ◽  
Dinesh Velayutham
Keyword(s):  
Rna Sequencing ◽  
Single Molecule ◽  
Transcriptome Assembly ◽  
Transcriptome Profiling ◽  
Read Length ◽  
Complex Nature ◽  
Disruptive Technology ◽  
Sequencing Technology ◽  
Sequencing Technologies ◽  
Long Read

Background: The standard approach for transcriptomic profiling involves high throughput short-read sequencing technology, mainly dominated by Illumina. However, the short reads have limitations in transcriptome assembly and in obtaining full-length transcripts due to the complex nature of transcriptomes with variable length and multiple alternative spliced isoforms. Recent advances in long read sequencing by the Oxford Nanopore Technologies (ONT) offered both cDNA as well as direct RNA sequencing and has brought a paradigm change in the sequencing technology to greatly improve the assembly and expression estimates. ONT enables molecules to be sequenced without fragmentation resulting in ultra-long read length enabling the entire genes and transcripts to be fully characterized. The direct RNA sequencing method, in addition, circumvents the reverse transcription and amplification steps. Objective: In this study, RNA sequencing methods were assessed by comparing data from Illumina (ILM), ONT cDNA (OCD) and ONT direct RNA (ODR). Methods: The sensitivity & specificity of the isoform detection was determined from the data generated by Illumina, ONT cDNA and ONT direct RNA sequencing technologies using Saccharomyces cerevisiae as model. Comparative studies were conducted with two pipelines to detect the isoforms, novel genes and variable gene length. Results: Mapping metrics and qualitative profiles for different pipelines are presented to understand these disruptive technologies. The variability in sequencing technology and the analysis pipeline were studied.

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