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Journal articles on the topic 'RNAseq analysis'

Author: Grafiati

Published: 2 November 2024

Last updated: 31 July 2025

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1

PAI, TUN-WEN, BO-HAN SU, PEI-CHIH WU, et al. "UNIQUE PEPTIDE IDENTIFICATION OF RNaseA SUPERFAMILY SEQUENCES BASED ON REINFORCED MERGING ALGORITHMS." Journal of Bioinformatics and Computational Biology 04, no. 01 (2006): 75–92. http://dx.doi.org/10.1142/s0219720006001710.

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Human ribonuclease A (RNaseA) superfamily consists of eight RNases with high similarity in which RNase2 and RNase3 share 76.7% identity. The evolutionary variation of RNases results in differential structures and functions of the enzymes. To distinguish the characteristics of each RNase, we developed reinforced merging algorithms (RMA) to rapidly identify the unique peptide motifs for each member of the highly conserved human RNaseA superfamily. Many motifs in RNase3 identified by RMA correlated well with the antigenic regions predicted by DNAStar. Two unique peptide motifs were experimentally

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Colombo, Anthony R., Timothy J. Triche Jr, and Giridharan Ramsingh. "Arkas: Rapid reproducible RNAseq analysis." F1000Research 6 (April 27, 2017): 586. http://dx.doi.org/10.12688/f1000research.11355.1.

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The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments. We offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata and calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The biologically informative downstream gene-set analysis maintains special focus

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Colombo, Anthony R., Timothy J. Triche Jr, and Giridharan Ramsingh. "Arkas: Rapid reproducible RNAseq analysis." F1000Research 6 (June 21, 2017): 586. http://dx.doi.org/10.12688/f1000research.11355.2.

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The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments. We offer cloud-scale RNAseq pipelines Arkas-Quantification, and Arkas-Analysis available within Illumina’s BaseSpace cloud application platform which expedites Kallisto preparatory routines, reliably calculates differential expression, and performs gene-set enrichment of REACTOME pathways. Due to inherit inefficiencies of scale, Illumina's BaseSpace computing platform offers a massively parallel distributive environment improving data management services and

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Lamping, Mario, Damian Tobias Rieke, Frederick Klauschen, et al. "Clinical impact of comprehensive versus targeted genomic analysis for precision oncology." Journal of Clinical Oncology 37, no. 15_suppl (2019): e13033-e13033. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13033.

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e13033 Background: Panel sequencing (PS) has become a standard-of-care in cancer diagnostics. More comprehensive analyses such as whole-exome (WES) or RNA sequencing (RNAseq) allow for the detection of rare and unknown genetic aberrations that are not covered by predefined assays. The clinical impact of targeted versus comprehensive genomic assays were analyzed in patients presented at the Charité Molecular Tumor Board (MTB). Methods: Patients (pts) with advanced and/or metastatic cancer for whom no standard therapy was available were discussed in the MTB to allocate diagnostic profiling and g

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Guo, Yan, Shilin Zhao, Chung-I. Li, Quanhu Sheng, and Yu Shyr. "RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment." Cancer Informatics 13s6 (January 2014): CIN.S17688. http://dx.doi.org/10.4137/cin.s17688.

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Sample size and power determination is the first step in the experimental design of a successful study. Sample size and power calculation is required for applications for National Institutes of Health (NIH) funding. Sample size and power calculation is well established for traditional biological studies such as mouse model, genome wide association study (GWAS), and microarray studies. Recent developments in high-throughput sequencing technology have allowed RNAseq to replace microarray as the technology of choice for high-throughput gene expression profiling. However, the sample size and power

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Guo, Yan, Shilin Zhao, Fei Ye, Quanhu Sheng, and Yu Shyr. "MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control." BioMed Research International 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/248090.

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Background. After a decade of microarray technology dominating the field of high-throughput gene expression profiling, the introduction of RNAseq has revolutionized gene expression research. While RNAseq provides more abundant information than microarray, its analysis has proved considerably more complicated. To date, no consensus has been reached on the best approach for RNAseq-based differential expression analysis. Not surprisingly, different studies have drawn different conclusions as to the best approach to identify differentially expressed genes based upon their own criteria and scenario

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Mora-Márquez, Fernando, José Luis Vázquez-Poletti, and Unai López de Heredia. "NGScloud2: optimized bioinformatic analysis using Amazon Web Services." PeerJ 9 (April 16, 2021): e11237. http://dx.doi.org/10.7717/peerj.11237.

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Background NGScloud was a bioinformatic system developed to perform de novo RNAseq analysis of non-model species by exploiting the cloud computing capabilities of Amazon Web Services. The rapid changes undergone in the way this cloud computing service operates, along with the continuous release of novel bioinformatic applications to analyze next generation sequencing data, have made the software obsolete. NGScloud2 is an enhanced and expanded version of NGScloud that permits the access to ad hoc cloud computing infrastructure, scaled according to the complexity of each experiment. Methods NGSc

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Kalinina, Alena, and Diane Lagace. "Single-Cell and Single-Nucleus RNAseq Analysis of Adult Neurogenesis." Cells 11, no. 10 (2022): 1633. http://dx.doi.org/10.3390/cells11101633.

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The complexity of adult neurogenesis is becoming increasingly apparent as we learn more about cellular heterogeneity and diversity of the neurogenic lineages and stem cell niches within the adult brain. This complexity has been unraveled in part due to single-cell and single-nucleus RNA sequencing (sc-RNAseq and sn-RNAseq) studies that have focused on adult neurogenesis. This review summarizes 33 published studies in the field of adult neurogenesis that have used sc- or sn-RNAseq methods to answer questions about the three main regions that host adult neural stem cells (NSCs): the subventricul

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Guo, Yan, Chung-I. Li, Fei Ye, and Yu Shyr. "Evaluation of read count based RNAseq analysis methods." BMC Genomics 14, Suppl 8 (2013): S2. http://dx.doi.org/10.1186/1471-2164-14-s8-s2.

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Zakharova, Galina, Maria Suntsova, Elizaveta Rabushko, et al. "A New Approach of Detecting ALK Fusion Oncogenes by RNA Sequencing Exon Coverage Analysis." Cancers 16, no. 22 (2024): 3851. http://dx.doi.org/10.3390/cancers16223851.

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Background: In clinical practice, various methods are used to identify ALK gene rearrangements in tumor samples, ranging from “classic” techniques, such as IHC, FISH, and RT-qPCR, to more advanced highly multiplexed approaches, such as NanoString technology and NGS panels. Each of these methods has its own advantages and disadvantages, but they share the drawback of detecting only a restricted (although sometimes quite extensive) set of preselected biomarkers. At the same time, whole transcriptome sequencing (WTS, RNAseq) can, in principle, be used to detect gene fusions while simultaneously a

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Penaherrera, Daniel, Sheri Skerget, Austin Christofferson, et al. "Development and Validation of a High Risk Multiple Myeloma Gene Expression Index from RNA Sequencing: An Mmrf Commpass Analysis." Blood 132, Supplement 1 (2018): 1895. http://dx.doi.org/10.1182/blood-2018-99-119610.

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Abstract Multiple Myeloma (MM) is a genetically heterogeneous disease of plasma cells that generally exhibits chromosomal abnormalities and distinct gene expression signatures. Previous studies have sought to identify gene expression indices using microarray technology to discern genes associated with survival outcomes to predict whether a newly diagnosed patient has an aggressive form of the disease. One such MM-specific index is the UAMS 70 gene index, which is composed of 51 over- and 19 under-expressed genes. This index was developed using Affymetrix U133Plus2.0 microarray data from 532 MM

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Metah, Chawin, Amal Khalifa, and Rebecca Palu. "A Parallel Computing Approach to Gene Expression and Phenotype Correlation for Identifying Retinitis Pigmentosa Modifiers in Drosophila." Computation 11, no. 6 (2023): 118. http://dx.doi.org/10.3390/computation11060118.

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As a genetic eye disorder, retinitis pigmentosa (RP) has been a focus of researchers to find a diagnosis through either genome-wide association (GWA) or RNAseq analysis. In fact, GWA and RNAseq are considered two complementary approaches to gaining a more comprehensive understanding of the genetics of different diseases. However, RNAseq analysis can provide information about the specific mechanisms underlying the disease and the potential targets for therapy. This research proposes a new approach to differential gene expression (DGE) analysis, which is the heart of the core-analysis phase in a

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Shiradkar, Rakesh, Tilak Pathak, Cynthia Winham, et al. "Abstract LB466: Visium-HD spatial RNAseq analysis of aggressive prostatic adenocarcinoma identifies distinct RNA signatures in metastatic and non-metastatic disease." Cancer Research 85, no. 8_Supplement_2 (2025): LB466. https://doi.org/10.1158/1538-7445.am2025-lb466.

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Abstract Background: There are limited studies regarding the tumor microenvironment of aggressive prostatic adenocarcinoma (PCa), at the single-cell level. In addition, there is a paucity of RNAseq data regarding gene expression of immune infiltrates and cancer-associated fibroblasts adjacent to PCa. The Visium-HD Spatial RNAseq platform sequences formalin-fixed paraffin embedded (FFPE) tissue using spatial barcodes at up to 2-micron pixel resolution, which achieves single-cell resolution. Design: We performed Visium-HD Spatial RNAseq analysis on FFPE blocks from radical prostatectomy specimen

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Dey, Narottam. "Global transcriptome analysis in rice (Oryza sativa. L) through RNASeq analysis." Canadian Journal of Biotechnology 1, Special Issue-Supplement (2017): 290. http://dx.doi.org/10.24870/cjb.2017-a274.

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Ogi, Derek A., and Sha Jin. "Transcriptome-Powered Pluripotent Stem Cell Differentiation for Regenerative Medicine." Cells 12, no. 10 (2023): 1442. http://dx.doi.org/10.3390/cells12101442.

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Pluripotent stem cells are endless sources for in vitro engineering human tissues for regenerative medicine. Extensive studies have demonstrated that transcription factors are the key to stem cell lineage commitment and differentiation efficacy. As the transcription factor profile varies depending on the cell type, global transcriptome analysis through RNA sequencing (RNAseq) has been a powerful tool for measuring and characterizing the success of stem cell differentiation. RNAseq has been utilized to comprehend how gene expression changes as cells differentiate and provide a guide to inducing

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Velichko, Sharlene, Johnathon Anderson, Stephanie Ryan, and Reen Wu. "Global gene expression analysis of Act1’s effects in airway epithelial cells (161.17)." Journal of Immunology 186, no. 1_Supplement (2011): 161.17. http://dx.doi.org/10.4049/jimmunol.186.supp.161.17.

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Abstract Act1/CIKS is an intracellular protein that has been shown to play an important role in mediating IL-17A and IL-25 signaling effects. Recently, defects in Act1 function and/or expression has been implicated in inflammatory disease, such as psoriatic arthritis and atopic dermatitis. We have found that the modulation of Act1 expression levels in human airway epithelial cells changes the expression levels of some genes, in the absence of cytokine stimulation. RNAseq is a powerful new technique to quantitatively measure changes at the transcriptome level. Here we describe the use of RNAseq

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Kim, Sunyoung, Jungwook Park, Ji Hyeon Kim, et al. "RNAseq-based Transcriptome Analysis of Burkholderia glumae Quorum Sensing." Plant Pathology Journal 29, no. 3 (2013): 249–59. http://dx.doi.org/10.5423/ppj.oa.04.2013.0044.

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Sun, Shiquan, Michelle Hood, Laura Scott, et al. "Differential expression analysis for RNAseq using Poisson mixed models." Nucleic Acids Research 45, no. 11 (2017): e106-e106. http://dx.doi.org/10.1093/nar/gkx204.

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Martell, Henry J., Avanthi Tayi Shah, Alex G. Lee, et al. "Abstract 54: Integrative analysis of whole-genome and RNA sequencing in high-risk pediatric malignancies." Cancer Research 82, no. 12_Supplement (2022): 54. http://dx.doi.org/10.1158/1538-7445.am2022-54.

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Abstract The use of sequencing-based assays for clinical management of pediatric cancer patients has become increasingly common. However, for many pediatric patients, gene panel based sequencing tests yield few actionable results. Given the complex genomic alterations present in many pediatric cancers, especially high-risk solid tumors, we hypothesized that an unbiased approach might reveal more actionable findings and lead to a more comprehensive understanding of these diseases. To accomplish this, we integrated whole-genome sequencing (WGS) with RNAseq in the analysis of a pediatric oncology

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Kim, Ji-Yeon, Kyunghee Park, Woong-Yang Park, et al. "Abstract P3-13-08: Fusion analysis including NTRK fusion in breast cancers (BC): From RNASeq data analysis from 629 BC tissue samples." Cancer Research 82, no. 4_Supplement (2022): P3–13–08—P3–13–08. http://dx.doi.org/10.1158/1538-7445.sabcs21-p3-13-08.

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Abstract Background: Neutrotrophin receptor tyrosine kinase (NTRK) gene fusions (NTRK1, NTRK2, or NTRK3) are oncogenic drivers of various tumor types. The NTRK fusion was detected in less than 5% of breast, colorectal, lung or any other types of cancers. However, large scaled next generation sequencing data for NTRK fusion in breast cancer have not existed. In this study, we performed RNASeq and fusion analysis including NTRK genes. Methods: We prospectively collected BC tumor tissues from the translational research conducted in Samsung Medical Center. Fusion was predicted from RNAseq using th

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Scheepbouwer, Chantal, Kayla Borland, Ernesto Aparicio, et al. "GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE." Neuro-Oncology 21, Supplement_6 (2019): vi110—vi111. http://dx.doi.org/10.1093/neuonc/noz175.462.

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Abstract BACKGROUND Diffuse lower grade gliomas (LGGs) are generally slow growing primary central nervous system tumors that occur in early adult life. The prevalence of isocitrate dehydrogenase (IDH) mutations is high in LGG, and induces excess production of the oncometabolite 2-hydroxyglutarate (2-HG). These gain-of-function mutations play a key role in promoting metabolic reprogramming of the cancer cell that affects activity of α-KG dependent demethylases. Inhibition of DNA demethylase activity leads to glioma with a CpG island methylator phenotype (G-CIMP). Whether the activity of RNA dem

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Kaisers , Wolfgang, Holger Schwender, and Heiner Schaal . "Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities." International Journal of Molecular Sciences 19, no. 11 (2018): 3687. http://dx.doi.org/10.3390/ijms19113687.

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We apply hierarchical clustering (HC) of DNA k-mer counts on multiple Fastq files. The tree structures produced by HC may reflect experimental groups and thereby indicate experimental effects, but clustering of preparation groups indicates the presence of batch effects. Hence, HC of DNA k-mer counts may serve as a diagnostic device. In order to provide a simple applicable tool we implemented sequential analysis of Fastq reads with low memory usage in an R package (seqTools) available on Bioconductor. The approach is validated by analysis of Fastq file batches containing RNAseq data. Analysis o

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Schuller, Dóra, Rik de Wijn, Dirk Pijnenburg, Tobias Deigner, Julia Schueler, and Simar Pal Singh. "Abstract LB060: Integrated analysis of transcriptomics and kinase activity data for better characterization of cancer models." Cancer Research 83, no. 8_Supplement (2023): LB060. http://dx.doi.org/10.1158/1538-7445.am2023-lb060.

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Abstract Introduction: Quantitative measurements of transcripts and proteins are key to investigate the basal state of a biological system, while functional proteomics inform about the active state of regulatory networks. Here we describe how the integration of transcriptomics and kinase activity data lead to a better characterization of various cancer models. Methods: We performed RNA sequencing (RNAseq) and kinase activity profiling of 63 Patient Derived Xenograft (PDX) models from six tumor types (Breast, Ovarian, Colon, Melanoma, Lung and Acute Myeloid Leukemia, AML). RNAseq was performed

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Jancalek, Radim, Frantisek Siegl, Jiri Sana, et al. "PATH-01. SMALL RNASEQ ANALYSIS OF MICRORNAS IN BRAIN METASTASIS." Neuro-Oncology 23, Supplement_6 (2021): vi115. http://dx.doi.org/10.1093/neuonc/noab196.454.

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Abstract MicroRNAs (miRNAs) are a well-known subclass of short non-coding RNAs responsible for posttranscriptional gene silencing and have been described as dysregulated in many cancers. They have also been shown to be both specific diagnostic, prognostic, and predictive biomarkers as well as therapeutic targets. Therefore, specific miRNA expression patterns of BMs of various origins could serve as a promising diagnostic tool for determining both the original tumor and the prognosis in patients with BMs of unknown origin. For identifying significantly dysregulated miRNAs among BMs (n=90) with

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Jancalek, Radim, Frantisek Siegl, Jiri Sana, et al. "BSCI-01. Small RNAseq analysis of microRNAs in brain metastasis." Neuro-Oncology Advances 3, Supplement_3 (2021): iii1. http://dx.doi.org/10.1093/noajnl/vdab071.000.

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Abstract MicroRNAs (miRNAs) are a well-known subclass of short non-coding RNAs responsible for posttranscriptional gene silencing and have been described as dysregulated in many cancers. They have also been shown to be both specific diagnostic, prognostic, and predictive biomarkers as well as therapeutic targets. Therefore, specific miRNA expression patterns of BMs of various origins could serve as a promising diagnostic tool for determining both the original tumor and the prognosis in patients with BMs of unknown origin. For identifying significantly dysregulated miRNAs among BMs (n = 90) wit

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Brettell, Schroeder, and Martin. "RNAseq Analysis Reveals Virus Diversity within Hawaiian Apiary Insect Communities." Viruses 11, no. 5 (2019): 397. http://dx.doi.org/10.3390/v11050397.

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Deformed wing virus (DWV) is the most abundant viral pathogen of honey bees and has been associated with large-scale colony losses. DWV and other bee-associated RNA viruses are generalists capable of infecting diverse hosts. Here, we used RNAseq analysis to test the hypothesis that due to the frequency of interactions, a range of apiary pest species would become infected with DWV and/or other honey bee-associated viruses. We confirmed that DWV-A was the most prevalent virus in the apiary, with genetically similar sequences circulating in the apiary pests, suggesting frequent inter-species tran

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Tariq, Muhammad A., Hyunsung J. Kim, Olufisayo Jejelowo, and Nader Pourmand. "Whole-transcriptome RNAseq analysis from minute amount of total RNA." Nucleic Acids Research 39, no. 18 (2011): e120-e120. http://dx.doi.org/10.1093/nar/gkr547.

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Beccuti, Marco, Francesca Cordero, Maddalena Arigoni, et al. "SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer." Bioinformatics 34, no. 5 (2017): 871–72. http://dx.doi.org/10.1093/bioinformatics/btx674.

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Marcotuli, Ilaria, Stefania Lucia Giove, Angelica Giancaspro, Agata Gadaleta, and Giuseppe Ferrara. "Dataset from RNAseq analysis of bud differentiation in Ficus carica." Data in Brief 50 (October 2023): 109418. http://dx.doi.org/10.1016/j.dib.2023.109418.

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Szeto, Christopher, Kevin Kazmierczak, Andrew Chambers, et al. "Comprehensive -omic analysis of 152 CRC patients allows greater subclassification than CMS or sidedness alone." Journal of Clinical Oncology 37, no. 4_suppl (2019): 601. http://dx.doi.org/10.1200/jco.2019.37.4_suppl.601.

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601 Background: Despite relatively high TMB in CRC, immune checkpoint inhibition (ICI) response is lower than in similarly mutated tissues such as melanoma (ORR 10-20% vs. 20-50%). MSI-status can be used to pre-select likely-responders, however MSI is rare. There is a need to guide ICI candidacy in CRC. Four transcriptomic-based CRC consensus molecular subtypes (CMS) have been described with ad hocclinical associations. We sought to confirm these subtypes in proteomic assays and their clinical associations. Methods: 152 CRC tumors from the National Cancer Centre Singapore were available for an

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Hafez, Ahmed Ibrahem, Beatriz Soriano, Aya Allah Elsayed, et al. "Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite." Genes 14, no. 2 (2023): 267. http://dx.doi.org/10.3390/genes14020267.

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The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called “RNASeq” and “VariantSeq” to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively. As such, “RNASeq” and “VariantSeq” are coupled with a Linux server infrastructure (named GPRO Server-Side) that hosts all dependencies of eac

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Collin, Lindsay Jane, Courtney E. Johnson, Natalie Davidson, Casey S. Greene, Joellen M. Schildkraut, and Jennifer A. Doherty. "Abstract 981: Validation of the ovarian tumor tissue analysis consortium stratified prognosis of ovarian tumors score using RNAseq and among Black women." Cancer Research 85, no. 8_Supplement_1 (2025): 981. https://doi.org/10.1158/1538-7445.am2025-981.

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Abstract Background: Ovarian cancer is highly fatal, and Black women are 30% more likely to die of ovarian cancer than white women. The Ovarian Tumor Tissue Analysis consortium Stratified Prognosis of Ovarian Tumors (OTTA-SPOT) gene expression signature demonstrates prognostic potential for high-grade serous ovarian cancers (HGSC) but was developed and validated in a predominately white population, using a NanoString assay. Translating the NanoString assay to RNA sequencing (RNAseq) data and replication across racial and ethnic groups will facilitate broader applications of the signature and i

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Hecht, Joel R., Patrick Grierson, Theodore H. Welling, et al. "Correlation of mesothelin (MSLN) expression measured by RNA sequencing (RNASeq) and immunohistochemistry (IHC) in MSLN-expressing tumors." Journal of Clinical Oncology 43, no. 4_suppl (2025): 766. https://doi.org/10.1200/jco.2025.43.4_suppl.766.

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766 Background: BASECAMP-1 (NCT04981119) is a pre-screening study to identify patients with tumor-associated human leukocyte antigen (HLA)-A*02 loss of heterozygosity (LOH) for interventional studies, such as EVEREST-2 (NCT06051695), a phase 1/2 study of logic-gated chimeric antigen receptor T-cell (CAR T) therapy for MSLN-expressing cancers. MSLN is a cell surface protein expressed in several cancer types, including mesothelioma (MESO), colorectal (CRC), non-small cell lung (NSCLC), ovarian (OVCA), and pancreatic (PANC) cancer, which can be associated with poor prognosis (1). Longitudinal cli

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Wong, Kwong-Kwok, Yvonne Tsang, and David M. Gershenson. "Abstract 4081: Analysis of low-grade serous ovarian cancer by long-read full length transcripts sequencing." Cancer Research 85, no. 8_Supplement_1 (2025): 4081. https://doi.org/10.1158/1538-7445.am2025-4081.

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Abstract Low grade serous ovarian carcinoma is a rare epithelial ovarian cancer that occurs more frequently in younger women. RNA sequencing (RNAseq) has been playing a pivotal role in understanding the molecular pathogenesis of the low-grade ovarian serous carcinoma (LGSOC). The quantification of gene expression with enough sequencing depth can be fairly accurate. However, the current short-read RNAseq approach is not very accurate in measuring individual transcript activity. This is because multiple transcripts from the same gene share high sequence similarity, which complicates the transcri

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Arora, Sonali, Nicholas Nuechterlein, Matt Jensen, et al. "EPCO-30. TRANSCRIPTOMIC ANALYSIS IDENTIFIES REGIONAL BIOLOGY AND OUTCOME HETEROGENEITY IN MEDULLOBLASTOMA AND EPENDYMOMA SUBTYPES." Neuro-Oncology 26, Supplement_8 (2024): viii8. http://dx.doi.org/10.1093/neuonc/noae165.0029.

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Abstract Medulloblastoma, the most common malignant pediatric brain tumor, includes four distinct subtypes: Wnt, Sonic Hedgehog (Shh), Group 3, and Group 4. In contrast, ependymomas, which account for 10% of pediatric brain tumors and 4% of adult brain tumors, are categorized into three types: supratentorial (ST), posterior fossa (PF), and spinal (SP). While molecular subgrouping has significantly advanced the classification of these diseases, the extent of heterogeneity within these subgroups remains unknown. To address this, we collected bulk RNA sequencing (RNASeq) data from 888 medulloblas

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Chen, Rui-Yi, Bui Thi Ngoc Hieu, Gilbert Audira, Bao Lou, Ming-Der Lin, and Chung-Der Hsiao. "Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles." Animals 10, no. 7 (2020): 1130. http://dx.doi.org/10.3390/ani10071130.

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Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the s

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Lee, Seul, Jae-Hwan Kim, Kwangmin Na, et al. "Abstract 6780: Characterization of immunological heterogeneity in the tumor microenvironment by integrated analyses using single cell RNAseq, spatial RNAseq and multiplex IHC." Cancer Research 83, no. 7_Supplement (2023): 6780. http://dx.doi.org/10.1158/1538-7445.am2023-6780.

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Abstract Heterogeneity in resistant to immunotherapies of tumor microenvironment (TME) has been implicated in immunotherapies to cause immune evasion or drug resistance. This study was conducted to explore the heterogeneity of TME through multiplex IHC, spatial and RNA sequencing analysis. We selected a sample from a lung adenocarcinoma patient without EGFR-activating mutation and expressing 30% of PD-L1. For quantitative analysis by multiplex IHC, various markers including CD4, CD8, FoxP3, granzyme B, CD20 and pan-cytokeratin were stained with 7 different fluorescence dyes, which was imaged w

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Yadav, Ruchi. "RNA-SEQ ANALYSIS TO EXPLORE THE VARIANTS IN MELANOMA CELLS: MOLECULAR DIAGNOSIS AND THERAPEUTICS." Journal of medical pharmaceutical and allied sciences 11, no. 3 (2022): 4869–80. http://dx.doi.org/10.55522/jmpas.v11i3.2930.

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High throughput sequencing technology that are also called as second generation or Next Generation (NGS) sequencing techniques has enabled researchers to study genome, transcriptome, metabolome of any organism in high throughput manner. RNA seq (Ribonucleic Acid Sequencing) is a NGS technique that is used to sequence total transcripts of cell and to study gene expression. This technique is widely used to identify differentially expressed genes and to identify variants. RNAseq technique has been used to study several diseases like cancers, neurological diseases, bacterial infections diseases an

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Macaulay, Charles W., Marcus R. Breese, and E. Alejandro Sweet-Cordero. "Abstract B011: Dynamics of predicted tumor neoepitope burden in a pan-cancer solid tumor pediatric cohort." Cancer Immunology Research 11, no. 12_Supplement (2023): B011. http://dx.doi.org/10.1158/2326-6074.tumimm23-b011.

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Abstract Human leukocyte antigen (HLA) binding of tumor neoepitopes confers clinical value in certain adult malignancies. However, the prevalence of tumors that result in HLA binding of neoepitopes in pediatric malignancies is not as well-characterized. We set out to establish the feasibility of predicting neoepitope burden and the prevalence of predicted neoepitope across a previously established cohort of pediatric oncology patients. Additionally, because this analysis requires knowledge of each patient’s HLA haplotype for predicting binding of tumor peptides, we also set out to develop a no

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Yadav, Shruti, Sean Daugherty, Amol Carl Shetty, and Ioannis Eleftherianos. "RNAseq Analysis of the Drosophila Response to the Entomopathogenic Nematode Steinernema." G3: Genes|Genomes|Genetics 7, no. 6 (2017): 1955–67. http://dx.doi.org/10.1534/g3.117.041004.

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Vedururu, Ravi kiran, Matthew J. Neave, Mary Tachedjian, et al. "RNASeq Analysis of Aedes albopictus Mosquito Midguts after Chikungunya Virus Infection." Viruses 11, no. 6 (2019): 513. http://dx.doi.org/10.3390/v11060513.

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Chikungunya virus (CHIKV) is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to a shift in vector preference towards Aedes albopictus. While mosquitoes are known to mount an antiviral immune response post-infection, molecular interactions during the course of infection at the tissue level remain largely uncharacterised. We performed whole transcriptome analysis on dissected midguts of Aedes albopictus infected with CHIKV to identify differentially expressed genes. For this, RNA was extract

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Valencia-Lozano, Eliana, Lisset Herrera-Isidrón, Jorge Abraham Flores-López, Osiel Salvador Recoder-Meléndez, Aarón Barraza, and José Luis Cabrera-Ponce. "Solanum tuberosum Microtuber Development under Darkness Unveiled through RNAseq Transcriptomic Analysis." International Journal of Molecular Sciences 23, no. 22 (2022): 13835. http://dx.doi.org/10.3390/ijms232213835.

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Potato microtuber (MT) development through in vitro techniques are ideal propagules for producing high quality potato plants. MT formation is influenced by several factors, i.e., photoperiod, sucrose, hormones, and osmotic stress. We have previously developed a protocol of MT induction in medium with sucrose (8% w/v), gelrite (6g/L), and 2iP as cytokinin under darkness. To understand the molecular mechanisms involved, we performed a transcriptome-wide analysis. Here we show that 1715 up- and 1624 down-regulated genes were involved in this biological process. Through the protein–protein interac

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Pushel, Irina, Lisa A. Lansdon, Byunggil Yoo, et al. "Short- and Long-Read RNA Sequencing Improve Molecular Profiling of Pediatric T-Cell Acute Lymphoblastic Leukemia." Blood 144, Supplement 1 (2024): 5921. https://doi.org/10.1182/blood-2024-208984.

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Acute lymphoblastic leukemia (ALL) is one of the most common pediatric cancers, accounting for approximately 1/3 of childhood cancer diagnoses. Of these patients, ~15% are diagnosed with T-cell ALL (T-ALL). Pediatric T-ALL is less well-characterized and has a worse prognosis than its B-cell counterpart, particularly after relapse. Although many genetic drivers for pediatric T-ALL have been characterized, this information does not currently inform treatment selection for patients. By integrating transcriptional profiling data with genomic findings from molecular and cytogenetic assays, we aim t

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Faltas, Bishoy, Rohan Bareja, Himisha Beltran, et al. "Integrated whole exome and RNA sequencing to reveal distinct genomic and transcriptomic landscape of upper tract urothelial carcinoma." Journal of Clinical Oncology 34, no. 2_suppl (2016): 379. http://dx.doi.org/10.1200/jco.2016.34.2_suppl.379.

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379 Background: Upper tract urothelial carcinoma (UTUC) represents up to 10% of all urothelial carcinoma (UC). UTUC is a lethal malignancy, with nearly one half the patients dying within 5 years. Our objective was to understand the biological differences between UTUC and bladder UC.Methods: Fresh frozen chemotherapy-naïve primary tumors from nephroureterectomy cases and corresponding germline samples underwent whole exome sequencing (WES) and RNA sequencing (RNAseq). The Cancer Genome Atlas (TCGA) WES and RNAseq raw data was reanalyzed through our in-house bioinformatic pipeline to compare the

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Morrison, Gareth, Alexander Cunha, Nita Jojo, et al. "Simple and rapid enrichment of circulating tumor cells (CTCs) for RNAseq in metastatic castrate resistant prostate cancer (mCRPC)." Journal of Clinical Oncology 37, no. 15_suppl (2019): e16587-e16587. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e16587.

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e16587 Background: CTCs have the potential to reflect not only genomic alterations but also cancer-relevant transcriptomic phenotypes. However, CTC gene expression has been hampered by signal-to-noise: rare CTC-derived transcripts are drowned out by abundant leukocyte-derived RNA. To date, a few specialized labs have achieved CTC RNAseq by capturing and analyzing single cells, a laborious and expensive approach not suitable for routine analysis of numerous samples. To address this need, we developed and validated a simple, rapid method for enrichment of live CTCs for RNAseq. Methods: Blood was

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Poddubskaya, Elena, Maxim Sorokin, Andrew Garazha, et al. "Clinical use of RNA sequencing and oncobox analytics to predict personalized targeted therapeutic efficacy." Journal of Clinical Oncology 38, no. 15_suppl (2020): e13676-e13676. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e13676.

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e13676 Background: Analysis of mutation profiles in cancer patients does not provide clinical benefits in 80-90% of cases in the US (Marquart et al., 2018). Gene expression analysis potentially complements standard detection of clinically relevant mutations. Methods: 239 adult late-stage cancer patients. RNA gene expression sequencing completed on solid tumor samples using FFPE blocks. Patient mRNA profiles were analyzed using Oncobox bioinformatics, prioritizing target drugs according to their personalized predicted efficacy. Summary reports were provided to oncologists and resulting treatmen

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Zhang, Zhen, Peilin Meng, Huijie Zhang, et al. "Brain Proteome-Wide Association Study Identifies Candidate Genes that Regulate Protein Abundance Associated with Post-Traumatic Stress Disorder." Genes 13, no. 8 (2022): 1341. http://dx.doi.org/10.3390/genes13081341.

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Although previous genome-wide association studies (GWASs) on post-traumatic stress disorder (PTSD) have identified multiple risk loci, how these loci confer risk of PTSD remains unclear. Through the FUSION pipeline, we integrated two human brain proteome reference datasets (ROS/MAP and Banner) with the PTSD GWAS dataset, respectively, to conduct a proteome-wide association study (PWAS) analysis. Then two transcriptome reference weights (Rnaseq and Splicing) were applied to a transcriptome-wide association study (TWAS) analysis. Finally, the PWAS and TWAS results were investigated through brain

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Padella, Antonella, Giorgia Simonetti, Viviana Guadagnuolo, et al. "Next-Generation Sequencing Analysis Revealed That BCL11B Chromosomal Translocation Cooperates with Point Mutations in the Pathogenesis of Acute Myeloid Leukemia." Blood 124, no. 21 (2014): 2352. http://dx.doi.org/10.1182/blood.v124.21.2352.2352.

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Abstract Whole exome and transcriptome sequencing (WES and RNAseq) technologies are able to provide a comprehensive analysis of the genomic aberrations acquired by malignant cells, of their synergistic effects and functional consequences. In particular, RNAseq enables the detection of gene fusions originating from rare chromosomal translocations that have been involved in the pathogenesis of Acute Myeloid Leukemia (AML). We performed WES and RNAseq of AML patients to identify novel genetic abnormalities playing a causative role in leukemia development. We collected bone marrow or peripheral bl

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Sasuclark, Alexandru R., Vedbar S. Khadka, and Matthew W. Pitts. "Cell-Type Specific Analysis of Selenium-Related Genes in Brain." Antioxidants 8, no. 5 (2019): 120. http://dx.doi.org/10.3390/antiox8050120.

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Selenoproteins are a unique class of proteins that play key roles in redox signaling in the brain. This unique organ is comprised of a wide variety of cell types that includes excitatory neurons, inhibitory neurons, astrocytes, microglia, and oligodendrocytes. Whereas selenoproteins are known to be required for neural development and function, the cell-type specific expression of selenoproteins and selenium-related machinery has yet to be systematically investigated. Due to advances in sequencing technology and investment from the National Institutes of Health (NIH)-sponsored BRAIN initiative,

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Martell, Henry J., Avanthi T. Shah, Alex G. Lee, et al. "Abstract 1759: Integrative longitudinal genomic analysis of therapy-resistant and metastatic pediatric cancers." Cancer Research 84, no. 6_Supplement (2024): 1759. http://dx.doi.org/10.1158/1538-7445.am2024-1759.

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Abstract Pediatric cancer patients are commonly profiled with gene-panel sequencing tests that yield few actionable results, in part due to the complex genomic alterations that define these malignancies. We hypothesized that integration of whole-genome (WGS) and RNA sequencing (RNAseq), would lead to a more comprehensive understanding of these diseases. Our study is uniquely focused on metastatic and relapsed disease, whereas previous studies focused on primary cases. We also prioritized longitudinal profiling, including with deep sequencing, to capture tumor evolution across primary and metas

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