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Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes

Yao Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu, Haiyun Wang
2021 BMC Genomics  
Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified  ...  Conclusions Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively.  ...  Availability of data and materials The datasets analysed during the current study are available in the Gene Expression Omnibus (GEO), [].  ... 
doi:10.1186/s12864-020-07318-y pmid:33407103 fatcat:huijz35w45gknj7ge4yoahipue

MOESM1 of Multiplatform biomarker identification using a data-driven approach enables single-sample classification

Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola
2019 Figshare  
in TCGA-LUAD RNA-Seq dataset .  ...  Figure S8 : S8 The expression heatmaps for signature genes between G3 (turquoise) and G4 (red) in GSE37418(A), GSE21140(B), and GSE37382(C). 8 Table S1 : S1 RNA-seq samples from Tumor-Educated Platelets  ... 
doi:10.6084/m9.figshare.10731242 fatcat:uuv5rzxjl5esjfr4psg752qpzi

Multiplatform biomarker identification using a data-driven approach enables single-sample classification

Ling Zhang, Ishwor Thapa, Christian Haas, Dhundy Bastola
2019 BMC Bioinformatics  
In this study, we present a simple, yet powerful data-driven method which contributes significantly to identification of robust cross-platform gene signature for disease classification of single-patient  ...  Validation with RNA-seq data of blood platelets shows that DDR achieves the superior performance in classification of six different tumor types as well as molecular target statuses (such as MET or HER2  ...  Fig. 1 1 Expression levels of five data-driven reference genes from TCGA-BRCA RNA-Seq samples and tiers classified based on reference genes (top).  ... 
doi:10.1186/s12859-019-3140-7 pmid:31752658 pmcid:PMC6868758 fatcat:43lcevqsvre7fludusjpcr3dce

Clarifying the Opaque: Identification of Direct Targets of Maize Opaque2:

Jennifer Mach
2015 The Plant Cell  
RNA-Seq identified ;1000 genes that show different transcript levels between wild-type and o2 endosperm; similarly, ChIP-Seq identified ;1000 genes with O2 binding sites.  ...  O2 encodes a bZIP transcription factor, and Li et al. (2015) combine RNA sequencing (RNA-Seq) based transcriptome analysis with chromatin immunoprecipitation sequencing (ChIP-Seq) analysis of protein binding  ...  RNA-Seq identified ;1000 genes that show different transcript levels between wild-type and o2 endosperm; similarly, ChIP-Seq identified ;1000 genes with O2 binding sites.  ... 
doi:10.1105/tpc.15.00156 pmid:25724643 pmcid:PMC4558677 fatcat:k45e3qdcdnapfcuzvpym2vxbpm

Shooting for the STARRs: a modified STARR-seq assay for rapid identification and evaluation of plant regulatory sequences in tobacco leaves

Matthias Benoit
2020 The Plant Cell  
A single genome gives rise to different cell types and organs in response to precise temporal and spatial regulation of gene expression, driven by developmental and environmental cues.  ...  The tobacco STARR-seq assay relies on reporter constructs driven by the 35S minimal promoter (green). Candidate enhancers (blue) are inserted at different positions within the construct.  ... 
doi:10.1105/tpc.20.00392 pmid:32434853 pmcid:PMC7346571 fatcat:s4dc6qcrprbfvhlatwxtpy7s6i

A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing

Karen Verboom, Wouter Van Loocke, Pieter-Jan Volders, Bieke Decaesteker, Francisco Avila Cobos, Simon Bornschein, Charles E. de Bock, Zeynep Kalender Atak, Emmanuelle Clappier, Stein Aerts, Jan Cools, Jean Soulier (+5 others)
2018 Haematologica  
(left) and total RNA-seq (right) (adjusted P-value <0.05).  ...  a similar gene expression profile. 13 By using polyA+ RNAseq data of 60 T-ALL patients (including 17 TLX positive cases) as well as total RNA-seq of 25 T-ALL patients (including 10 TLX positive cases  ...  and a primary T-ALL patient cohort, we also identified 144 putative TLX-specific oncogenic lncRNAs, which could be further tested for phenotypic effects upon knockdown and explored as new targets for RNA-based  ... 
doi:10.3324/haematol.2018.190587 pmid:29954933 fatcat:son4nkwmh5f6doa5n3cvte6shq

Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease [article]

Samya Chakravorty, Kiera Berger, Laura Rufibach, Logan Gloster, Sarah Emmons, Sreekala Shenoy, Madhuri Hegde, Ashok Reddy Dinasarapu, Greg Gibson
2021 medRxiv   pre-print
364 Dysferlinopathy/related-LGMD-suspected patient-cohort without complete molecular-diagnosis or genotype-phenotype correlation; and then combined with blood-based targeted-transcriptome-sequencing (RNA-Seq  ...  Results Our combinatorial-approach significantly increased the diagnostic-yield from 25% (N=326; 18%-27%; 95%CI) to 82% (N=38; 69.08% to 84.92%; 95% CI) by combining monocyte-assay with enhanced-RNA-Seq-analysis  ...  274 gene-panel (Table S1) RNA-Seq ( Fig. 1A and 1C ) was used.  ... 
doi:10.1101/2021.01.14.21249850 fatcat:q7f6lnaocngidcawbbigubjfyy

Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

Ao Zhou, Marcus R Breese, Yangyang Hao, Howard J Edenberg, Lang Li, Todd C Skaar, Yunlong Liu
2012 BMC Genomics  
Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing.  ...  We further applied Alt Event Finder on a set of RNA-seq data from rat liver tissues, and identified dozens of novel cassette exon events whose splicing patterns changed after extensive alcohol exposure  ...  Methods Dataset RNA-seq dataset We used two RNA-seq datasets for de novo alternative splicing event identification, human hepatocytes and rat liver cells.  ... 
doi:10.1186/1471-2164-13-s8-s10 pmid:23281921 pmcid:PMC3535697 fatcat:jm3zmg54lrfffcgoqaix26kuyy

Genomic profiling of Nipah virus using NGS driven RNA-Seq expression data

Md. Zakiul Hassan, Infectious Diseases Division, icddr,b (International Centre for Diarrheal Disease Research, Bangladesh), Dhaka, Bangladesh
2019 Bioinformation  
We analyzed the NGS RNA-Seq gene expression data of NiV to detect differentially expressed genes (DEGs) using the statistical R package limma.  ...  We used the Cytoscape, Ensembl, and STRING tools to construct the gene-gene interaction tree, phylogenetic gene tree and protein-protein interaction networks towards functional annotation.  ...  Identification of differentially expressed genes from the large scale NGS RNA-Seq data and functional annotation of the Nipah virus were the key objectives of this study.  ... 
doi:10.6026/97320630015853 pmid:32256005 pmcid:PMC7088422 fatcat:imqjiqf5dfg2rbianz2wuuf7o4

Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling

Stinus Lindgreen, Sinan Uğur Umu, Alicia Sook-Wei Lai, Hisham Eldai, Wenting Liu, Stephanie McGimpsey, Nicole E. Wheeler, Patrick J. Biggs, Nick R. Thomson, Lars Barquist, Anthony M. Poole, Paul P. Gardner (+1 others)
2014 PLoS Computational Biology  
The emergence of new technologies for characterizing transcriptome outputs, notably RNA-seq, are improving noncoding RNA identification and expression quantification.  ...  Noncoding RNAs are integral to a wide range of biological processes, including translation, gene regulation, host-pathogen interactions and environmental sensing.  ...  Identification of novel RNAs From the mapped RNA-seq data, potential novel RNA genes (designated RNAs of Unknown Function, or RUFs) were picked manually by locating regions in the genomes that showed high  ... 
doi:10.1371/journal.pcbi.1003907 pmid:25357249 pmcid:PMC4214555 fatcat:a2w47pjtsjgzfoy6f4hi37spce

Enhancement of Transgene Expression by Mild Hypothermia Is Promoter Dependent in HEK293 Cells

Min Ho Jang, Honggi Min, Jae Seong Lee
2021 Life  
EGFP expression driven by the CMV promoter increased up to 1.5-fold at 32 °C versus 37 °C under stable expression, while others showed no hypothermic response.  ...  CMV-enhancer-specific transcription factors (TFs) were then predicted through in silico analysis and RNA-sequencing analysis, resulting in the selection of one TF, NKX3-1.  ...  Figure 2 . 2 Identification of CMV-enhancer specific transcription factors (TFs): (A) heat map of the RNA-seq data.  ... 
doi:10.3390/life11090901 pmid:34575051 fatcat:5ek3fyjojnha5oq64b4pabfv7y

Biogenesis, identification, and function of exonic circular RNAs

Iju Chen, Chia-Ying Chen, Trees-Juen Chuang
2015 Wiley Interdisciplinary Reviews - RNA  
But recently, rapid advances in high-throughput RNA sequencing (RNA-seq) for global investigation of nonco-linear (NCL) RNAs, which comprised sequence segments that are topologically inconsistent with  ...  To date, thousands of ecircRNAs have been identified in multiple tissues/cell types from diverse species, through analyses of RNA-seq data.  ...  IDENTIFICATION OF EXONIC CIRCRNAS Strategies to Identify ecircRNAs Many RNA-seq-based bioinformatics tools have been developed to identify ecircRNA candidates.  ... 
doi:10.1002/wrna.1294 pmid:26230526 pmcid:PMC5042038 fatcat:h3fiyjen3jdyti3e4tzcu4bzxe

Advancing clinical genomics and precision medicine with GVViZ: FAIR bioinformatics platform for variable gene-disease annotation, visualization, and expression analysis

Zeeshan Ahmed, Eduard Gibert Renart, Saman Zeeshan, XinQi Dong
2021 Human Genomics  
GVViZ is a user-friendly, cross-platform, and database application for RNA-seq-driven variable and complex gene-disease data annotation and expression analysis with a dynamic heat map visualization.  ...  Conclusions We emphasize that automated and interactive visualization should be an indispensable component of modern RNA-seq analysis, which is currently not the case.  ...  ZA modeled and created the gene-disease annotation and RNA-seq gene expression databases, integrated with GVViZ. SZ participated in the performance evaluation and experiments using GVViZ.  ... 
doi:10.1186/s40246-021-00336-1 pmid:34174938 pmcid:PMC8235866 fatcat:rejj7qf3kfcrddao3cw5cpeubm

Translational control of cardiac fibrosis [article]

Sonia Chothani, Sebastian Schafer, Eleonora Adami, Sivakumar Viswanathan, Anissa A Widjaja, Sarah R Langley, Jessie Tan, Chee Jian Pua, Giuseppe D'Agostino, Sebastiaan van Heesch, Franziska Witte, Leanne E Felkin (+8 others)
2018 bioRxiv   pre-print
We then used miRNA-and RNA-binding protein-based analyses to identify translational regulators of fibrogenic genes.  ...  Targets of RNA-binding proteins were strongly enriched in post-transcriptionally regulated genes, suggesting genes such as MBNL2 can act as translational activators or repressors.  ...  Data and software availability The data is available on the gene expression omnibus (GEO id. pending) In order to investigate transcription and translation levels of individual genes we provide a web-resource  ... 
doi:10.1101/451666 fatcat:uwhtz7u3sbe3nhqehw2cc6on5a

Identifying transcription start sites and active enhancer elements using BruUV-seq

Brian Magnuson, Artur Veloso, Killeen S. Kirkconnell, Leonardo Carmo de Andrade Lima, Michelle T. Paulsen, Emily A. Ljungman, Karan Bedi, Jayendra Prasad, Thomas E. Wilson, Mats Ljungman
2015 Scientific Reports  
′-end of genes promoting the identification of transcription start sites (TSSs).  ...  Finally, BruUV-seq identified putative enhancer elements induced by tumor necrosis factor (TNF) treatment concomitant with expression of nearby TNF-induced genes.  ...  We found examples of gene clusters driven by individual promoters (Supplementary Fig. 3a) as well as gene clusters driven by a single TSS ( Supplementary Fig. 3b,c) .  ... 
doi:10.1038/srep17978 pmid:26656874 pmcid:PMC4675984 fatcat:m4ixxls53fcsfea54xebaogb4e
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