scholarly journals Systematic Selection of Reference Genes for the Normalization of Circulating RNA Transcripts in Pregnant Women Based on RNA-Seq Data

2017 ◽  
Vol 18 (8) ◽  
pp. 1709 ◽  
Author(s):  
Stephen Chim ◽  
Karen Wong ◽  
Claire Chung ◽  
Stephanie Lam ◽  
Jamie Kwok ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Reference Genes ◽  
Rna Seq ◽  
Rna Transcripts ◽  
Systematic Selection ◽  
Circulating Rna ◽  
Selection Of

scholarly journals Systematic selection of reference genes for normalization of circulating RNA transcripts in pregnant women based on RNA-seq data

2017 ◽  
Author(s):  
Stephen S. C. Chim ◽  
Karen K. W. Wong ◽  
Claire Y. L. Chung ◽  
Stephanie K. W. Lam ◽  
Jamie S. L. Kwok ◽  
...  
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Maternal Blood ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Blood Samples ◽  
Rna Transcripts ◽  
Starting Point ◽  
Circulating Rna ◽  
Whole Transcriptome

AbstractRNA transcripts circulating in peripheral blood represent an important source of non-invasive biomarkers. To accurately quantify the levels of a circulating transcript, one needs to normalize the data with internal control reference genes, which are detected at relatively constant levels across different blood samples. A few stably-expressed reference gene candidates have to be selected from transcriptome data before validation of their stable expression by reverse-transcription quantitative polymerase chain reaction. However, there is a lack of transcriptome, let alone whole-transcriptome, data from maternal blood. To overcome this shortfall, we performed RNA-seq on blood samples from women presented with preterm labor. Of 11215 exons detected in the maternal blood whole-transcriptome, we systematically identified a panel of 395 genes comprising exons that were detected at acoefficient of variation(CV) ranging from 7.75%-17.7%. Their levels were considerably less variable than anyGAPDHexon (minimumCV, 27.3%). Upon validation, selected genes from this panel remained as more stably expressed thanGAPDHin maternal blood. This panel is over-represented with genes involved with actin cytoskeleton, macromolecular complex and the integrin signaling pathway. This groundwork provides a starting point for systematically selecting reference gene candidates for normalizing the levels of circulating RNA transcripts in maternal blood.

scholarly journals RNA‐seq‐based selection of reference genes for RT‐qPCR analysis of pitaya

FEBS Open Bio ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1403-1412 ◽  
Author(s):  
Quandong Nong ◽  
Yongchao Yang ◽  
Mingyong Zhang ◽  
Mei Zhang ◽  
Jiantong Chen ◽  
...  
Keyword(s):  
Reference Genes ◽  
Rna Seq ◽  
Qpcr Analysis ◽  
Selection Of

Selection of reference genes for quantitative real-time PCR in six oil-tea camellia based on RNA-seq

2013 ◽  
Vol 47 (6) ◽  
pp. 836-851 ◽  
Author(s):  
C. F. Zhou ◽  
P. Lin ◽  
X. H. Yao ◽  
K. L. Wang ◽  
J. Chang ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Reference Genes ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Selection Of

scholarly journals Genome-wide identification of new reference genes for RT-qPCR normalization in CGMMV-infected Lagenaria siceraria

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5642 ◽  
Author(s):  
Chenhua Zhang ◽  
Hongying Zheng ◽  
Xinyang Wu ◽  
Heng Xu ◽  
Kelei Han ◽  
...  
Keyword(s):  
Reference Genes ◽  
Bottle Gourd ◽  
Lagenaria Siceraria ◽  
Rna Seq ◽  
Isopentenyl Transferase ◽  
Genome Wide ◽  
Transcriptome Database ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Selection Of

Lagenaria siceraria is an economically important cucurbitaceous crop, but suitable reference genes (RGs) to use when the plants are infected by cucumber green mottle mosaic virus (CGMMV) have not been determined. Sixteen candidate RGs of both leaf and fruit and 18 candidate RGs mostly from separate RNA-Seq datasets of bottle gourd leaf or fruit were screened and assessed by RT-qPCR. The expression stability of these genes was determined and ranked using geNorm, NormFinder, BestKeeper and RefFinder. Comprehensive analysis resulted in the selection of LsCYP, LsH3, and LsTBP as the optimal RGs for bottle gourd leaves, and LsP4H, LsADP, and LsTBP for fruits. LsWD, LsGAPDH, and LsH3 were optimal for use in both leaves and fruits under the infection of CGMMV. Isopentenyl transferase (IPT) and DNA-directed RNA polymerase (DdRP) were used to validate the applicability of the most stable identified RGs from bottle gourd in response to CGMMV. All the candidate RGs performed in RT-qPCR consistently with the data from the transcriptome database. The results demonstrated that LsWD, LsGAPDH and LsH3 were the most suitable internal RGs for the leaf, and LsH3, LsGAPDH, LsP4H and LsCYP for the fruit.

scholarly journals Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Katerina Jureckova ◽  
Hana Raschmanova ◽  
Jan Kolek ◽  
Maryna Vasylkivska ◽  
Barbora Branska ◽  
...  
Keyword(s):  
Reference Genes ◽  
Enrichment Analysis ◽  
Clostridium Beijerinckii ◽  
Stable Expression ◽  
Rna Seq ◽  
Go Enrichment ◽  
Qpcr Normalization ◽  
Suitable Reference ◽  
Go Enrichment Analysis ◽  
Selection Of

Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.

scholarly journals Putative transmembrane transporter modulates higher-level aggression in Drosophila

2017 ◽  
Vol 114 (9) ◽  
pp. 2373-2378 ◽  
Author(s):  
Budhaditya Chowdhury ◽  
Yick-Bun Chan ◽  
Edward A. Kravitz
Keyword(s):  
Causal Effect ◽  
Nerve Terminals ◽  
Rna Seq ◽  
Wild Type ◽  
Temperature Dependent ◽  
Number Of Genes ◽  
Interesting Family ◽  
Solute Carrier ◽  
Transmembrane Transporter ◽  
Selection Of

By selection of winners of dyadic fights for 35 generations, we have generated a hyperaggressive Bully line of flies that almost always win fights against the parental wild-type Canton-S stock. Maintenance of the Bully phenotype is temperature dependent during development, with the phenotype lost when flies are reared at 19 °C. No similar effect is seen with the parent line. This difference allowed us to carry out RNA-seq experiments and identify a limited number of genes that are differentially expressed by twofold or greater in the Bullies; one of these was a putative transmembrane transporter, CG13646, which showed consistent and reproducible twofold down-regulation in Bullies. We examined the causal effect of this gene on the phenotype with a mutant line for CG13646, and with an RNAi approach. In all cases, reduction in expression of CG13646 by approximately half led to a hyperaggressive phenotype partially resembling that seen in the Bully flies. This gene is a member of a very interesting family of solute carrier proteins (SLCs), some of which have been suggested as being involved in glutamine/glutamate and GABA cycles of metabolism in excitatory and inhibitory nerve terminals in mammalian systems.

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