scholarly journals Plasmodium parasites mount an arrest response to dihydroartemisinin, as revealed by whole transcriptome shotgun sequencing (RNA-seq) and microarray study

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Philip J. Shaw ◽  
Sastra Chaotheing ◽  
Pavita Kaewprommal ◽  
Jittima Piriyapongsa ◽  
Chayaphat Wongsombat ◽  
...  
Keyword(s):  
Shotgun Sequencing ◽  
Rna Seq ◽  
Microarray Study ◽  
Whole Transcriptome

scholarly journals Whole-Transcriptome Shotgun Sequencing (RNA-seq) Screen Reveals Upregulation of Cellobiose and Motility Operons of Lactobacillus ruminis L5 during Growth on Tetrasaccharides Derived from Barley β-Glucan

2013 ◽  
Vol 79 (18) ◽  
pp. 5661-5669 ◽  
Author(s):  
Blair Lawley ◽  
Ian M. Sims ◽  
Gerald W. Tannock
Keyword(s):  
Growth Phase ◽  
Shotgun Sequencing ◽  
Rna Seq ◽  
Content Type ◽  
Batch Cultures ◽  
Reverse Transcription Quantitative Pcr ◽  
Altered Gene ◽  
Lactobacillus Ruminis ◽  
Early Growth Phase ◽  
Whole Transcriptome

ABSTRACTLactobacillus ruminisis an inhabitant of human bowels and bovine rumens. None of 10 isolates (three from bovine rumen, seven from human feces) ofL. ruministhat were tested could utilize barley β-glucan for growth. Seven of the strains ofL. ruminiswere, however, able to utilize tetrasaccharides (3-O-β-cellotriosyl-d-glucose [LDP4] or 4-O-β-laminaribiosyl-d-cellobiose [CDP4]) present in β-glucan hydrolysates for growth. The tetrasaccharides were generated by the use of lichenase or cellulase, respectively. To learn more about the utilization of tetrasaccharides byL. ruminis, whole-transcriptome shotgun sequencing (RNA-seq) was tested as a transcriptional screen to detect altered gene expression when an autochthonous human strain (L5) was grown in medium containing CDP4. RNA-seq results were confirmed and extended by reverse transcription-quantitative PCR assays of selected genes in two upregulated operons when cells were grown as batch cultures in medium containing either CDP4 or LDP4. The cellobiose utilization operon had increased transcription, particularly in early growth phase, whereas the chemotaxis/motility operon was upregulated in late growth phase. Phenotypic changes were seen in relation to upregulation of chemotaxis/flagellar operons: flagella were rarely seen by electron microscopy on glucose-grown cells but cells cultured in tetrasaccharide medium were commonly flagellated. Chemotactic movement toward tetrasaccharides was demonstrated in capillary cultures.L. ruminisutilized 3-O-β-cellotriosyl-d-glucose released by β-glucan hydrolysis due to bowel commensalCoprococcussp., indicating that cross feeding of tetrasaccharide between bacteria could occur. Therefore, the RNA-seq screen and subsequent experiments had utility in revealing foraging attributes of gut commensalLactobacillus ruminis.

scholarly journals MOLECULAR SIGNATURES OF LUNG CANCER BASED ON GENE EXPRESSION RANKING OF RNA-SEQ DATA

2015 ◽  
Author(s):  
V. Bondarenko ◽  
Frank Emmert-Streib
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Transcriptome Analysis ◽  
Shotgun Sequencing ◽  
Experimental Methodology ◽  
Molecular Signatures ◽  
Rna Seq ◽  
Disease Biomarkers ◽  
Whole Transcriptome ◽  
Individual Human

<p>Whole Transcriptome Shotgun Sequencing or RNA-Seq is an experimental methodology which allows quantification of all transcripts expressed in a population of cells. In biomedicine, it is gradually gaining popularity to become a prevalent method<br />for transcriptome analysis. Sequencing of individual human transcriptomes has become a powerful tool in disease biomarkers discovery and setting up individual<br />treatment therapy of cancer and other disorders.</p>

scholarly journals Impact of RNA Extraction and Target Capture Methods on RNA Sequencing Using Formalin-Fixed, Paraffin Embedded Tissues

2019 ◽  
Author(s):  
Christopher A. Hilker ◽  
Aditya V. Bhagwate ◽  
Jin Sung Jang ◽  
Jeffrey G Meyer ◽  
Asha A. Nair ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fusion Gene ◽  
Rna Extraction ◽  
Extraction Methods ◽  
Rna Seq ◽  
Gene Detection ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Whole Transcriptome ◽  
Formalin Fixed

AbstractFormalin fixed paraffin embedded (FFPE) tissues are commonly used biospecimen for clinical diagnosis. However, RNA degradation is extensive when isolated from FFPE blocks making it challenging for whole transcriptome profiling (RNA-seq). Here, we examined RNA isolation methods, quality metrics, and the performance of RNA-seq using different approaches with RNA isolated from FFPE and fresh frozen (FF) tissues. We evaluated FFPE RNA extraction methods using six different tissues and five different methods. The reproducibility and quality of the prepared libraries from these RNAs were assessed by RNA-seq. We next examined the performance and reproducibility of RNA-seq for gene expression profiling with FFPE and FF samples using targeted (Kinome capture) and whole transcriptome capture based sequencing. Finally, we assessed Agilent SureSelect All-Exon V6+UTR capture and the Illumina TruSeq RNA Access protocols for their ability to detect known gene fusions in FFPE RNA samples. Although the overall yield of RNA varied among extraction methods, gene expression profiles generated by RNA-seq were highly correlated (>90%) when the input RNA was of sufficient quality (≥DV200 30%) and quantity (≥ 100 ng). Using gene capture, we observed a linear relationship between gene expression levels for shared genes that were captured using either All-Exon or Kinome kits. Gene expression correlations between the two capture-based approaches were similar using RNA from FFPE and FF samples. However, TruSeq RNA Access protocol provided significantly higher exon and junction reads when compared to the SureSelect All-Exon capture kit and was more sensitive for fusion gene detection. Our study established pre and post library construction QC parameters that are essential to reproducible RNA-seq profiling using FFPE samples. We show that gene capture based NGS sequencing is an efficient and highly reproducible strategy for gene expression measurements as well as fusion gene detection.

scholarly journals ‘Meiotic genes’ are constitutively expressed in an asexual amoeba and are not necessarily involved in sexual reproduction

2019 ◽  
Vol 15 (3) ◽  
pp. 20180871 ◽  
Author(s):  
Sutherland K. Maciver ◽  
Zisis Koutsogiannis ◽  
Alvaro de Obeso Fernández del Valle
Keyword(s):  
Homologous Recombination ◽  
Sexual Reproduction ◽  
Asexual Reproduction ◽  
Shotgun Sequencing ◽  
Ancestral State ◽  
Rna Seq ◽  
Next Generation ◽  
Related Process

The amoebae (and many other protists) have traditionally been considered as asexual organisms, but suspicion has been growing that these organisms are cryptically sexual or are at least related to sexual lineages. This contention is mainly based on genome studies in which the presence of ‘meiotic genes’ has been discovered. Using RNA-seq (next-generation shotgun sequencing, identifying and quantifying the RNA species in a sample), we have found that the entire repertoire of meiotic genes is expressed in exponentially growing Acanthamoeba and we argue that these so-called meiotic genes are involved in the related process of homologous recombination in this amoeba. We contend that they are only involved in meiosis in other organisms that indulge in sexual reproduction and that homologous recombination is important in asexual protists as a guard against the accumulation of mutations. We also suggest that asexual reproduction is the ancestral state.

scholarly journals Stranded Whole Transcriptome RNA‐Seq for All RNA Types

2015 ◽  
Vol 84 (1) ◽  
Author(s):  
David F.B. Miller ◽  
Pearlly X. Yan ◽  
Fang Fang ◽  
Aaron Buechlein ◽  
James B. Ford ◽  
...  
Keyword(s):  
Rna Seq ◽  
Whole Transcriptome

scholarly journals Screening of Virulence-Related Transcriptional Regulators in Streptococcus suis

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 972
Author(s):  
Liang Liu ◽  
Qiang Zhang ◽  
Zhongmin Xu ◽  
Bo Chen ◽  
Anding Zhang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Streptococcus Suis ◽  
Transcriptional Regulators ◽  
Rna Seq ◽  
Related Factors ◽  
Transcriptional Regulatory ◽  
Mutant Strains ◽  
Whole Transcriptome

Streptococcus suis (S.suis) is an important zoonotic pathogen that causes many severe diseases in pigs and humans. Virulence-related transcriptional regulators have been widely reported in pathogenic microorganisms, but only a few have been identified in S.suis. Our aim was to screen virulence-related transcriptional regulators in S.suis. A total of 89 such genes were predicted in the S.suis genome, of which 22 were up-regulated and 18 were down-regulated during S.suis infection in mice. To evaluate the roles of these differentially expressed factors in S.suis virulence, deletion mutants were constructed, and 10 mutants were successfully obtained. Among these genes, the deletion of comR, sitR, or sxvR caused significantly decreased virulence in mice, compared to that with the wild-type strain. Moreover, the survival of ΔcomR, ΔsitR, and ΔsxvR mutant strains in blood was significantly reduced both in vitro and in vivo. Furthermore, their pro-inflammatory abilities were also obviously decreased in vivo. The regulatory mechanisms of comR, sitR, and sxvR were then analyzed by whole transcriptome RNA sequencing (RNA-Seq). Results indicated that the absence of comR induced the down-regulation of 17 virulence factors or virulence-related factors, including genes involved in the synthesis of capsules, oxidative stress tolerance, immune evasion, and cell division. Furthermore, three and two virulence factors or virulence-related factors were down-regulated upon deletion of sitR and sxvR, respectively. Thus, this study reports the discovery of three virulence-associated transcriptional regulatory factors in S.suis. These factors could ultimately be targeted to control infection caused by these bacteria.

scholarly journals CoCo: RNA-seq read assignment correction for nested genes and multimapped reads

2019 ◽  
Vol 35 (23) ◽  
pp. 5039-5047 ◽  
Author(s):  
Gabrielle Deschamps-Francoeur ◽  
Vincent Boivin ◽  
Sherif Abou Elela ◽  
Michelle S Scott
Keyword(s):  
Supplementary Information ◽  
Rna Seq ◽  
Non Coding Rna ◽  
Abundance Estimates ◽  
Gene Coverage ◽  
Nested Genes ◽  
Quantification Accuracy ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
Generation Sequencing

Abstract Motivation Next-generation sequencing techniques revolutionized the study of RNA expression by permitting whole transcriptome analysis. However, sequencing reads generated from nested and multi-copy genes are often either misassigned or discarded, which greatly reduces both quantification accuracy and gene coverage. Results Here we present count corrector (CoCo), a read assignment pipeline that takes into account the multitude of overlapping and repetitive genes in the transcriptome of higher eukaryotes. CoCo uses a modified annotation file that highlights nested genes and proportionally distributes multimapped reads between repeated sequences. CoCo salvages over 15% of discarded aligned RNA-seq reads and significantly changes the abundance estimates for both coding and non-coding RNA as validated by PCR and bedgraph comparisons. Availability and implementation The CoCo software is an open source package written in Python and available from http://gitlabscottgroup.med.usherbrooke.ca/scott-group/coco. Supplementary information Supplementary data are available at Bioinformatics online.

Sign in / Sign up

Export Citation Format

Share Document