Relevant bibliographies by topics / Small RNA-Seq

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Small RNA-Seq'

Author: Grafiati
Published: 4 June 2021
Last updated: 22 June 2024

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Journal articles on the topic "Small RNA-Seq"

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Hagemann-Jensen, Michael, Ilgar Abdullayev, Rickard Sandberg, and Omid R. Faridani. "Small-seq for single-cell small-RNA sequencing." Nature Protocols 13, no. 10 (September 24, 2018): 2407–24. http://dx.doi.org/10.1038/s41596-018-0049-y.

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Alisoltani, Arghavan, Hossein Fallahi, Behrouz Shiran, Anousheh Alisoltani, and Esmaeil Ebrahimie. "RNA-Seq SSRs and small RNA-Seq SSRs: New approaches in cancer biomarker discovery." Gene 560, no. 1 (April 2015): 34–43. http://dx.doi.org/10.1016/j.gene.2015.01.027.

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Solaguren-Beascoa, Maria, Ana Gámez-Valero, Georgia Escaramís, Marina Herrero-Lorenzo, Ana M. Ortiz, Carla Minguet, Ricardo Gonzalo, Maria Isabel Bravo, Montserrat Costa, and Eulàlia Martí. "Phospho-RNA-Seq Highlights Specific Small RNA Profiles in Plasma Extracellular Vesicles." International Journal of Molecular Sciences 24, no. 14 (July 19, 2023): 11653. http://dx.doi.org/10.3390/ijms241411653.

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Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5′-end (5′-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
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Xu, Zhongneng, and Shuichi Asakawa. "Physiological RNA dynamics in RNA-Seq analysis." Briefings in Bioinformatics 20, no. 5 (June 29, 2018): 1725–33. http://dx.doi.org/10.1093/bib/bby045.

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Abstract Physiological RNA dynamics cause problems in transcriptome analysis. Physiological RNA accumulation affects the analysis of RNA quantification, and physiological RNA degradation affects the analysis of the RNA sequence length, feature site and quantification. In the present article, we review the effects of physiological degradation and accumulation of RNA on analysing RNA sequencing data. Physiological RNA accumulation and degradation probably led to such phenomena as incorrect estimations of transcription quantification, differential expressions, co-expressions, RNA decay rates, alternative splicing, boundaries of transcription, novel genes, new single-nucleotide polymorphisms, small RNAs and gene fusion. Thus, the transcriptomic data obtained up to date warrant further scrutiny. New and improved techniques and bioinformatics software are needed to produce accurate data in transcriptome research.
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Zhou, Weiqiang, Zhicheng Ji, Weixiang Fang, and Hongkai Ji. "Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq." Nucleic Acids Research 47, no. 19 (August 20, 2019): e121-e121. http://dx.doi.org/10.1093/nar/gkz716.

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Abstract Conventional high-throughput genomic technologies for mapping regulatory element activities in bulk samples such as ChIP-seq, DNase-seq and FAIRE-seq cannot analyze samples with small numbers of cells. The recently developed low-input and single-cell regulome mapping technologies such as ATAC-seq and single-cell ATAC-seq (scATAC-seq) allow analyses of small-cell-number and single-cell samples, but their signals remain highly discrete or noisy. Compared to these regulome mapping technologies, transcriptome profiling by RNA-seq is more widely used. Transcriptome data in single-cell and small-cell-number samples are more continuous and often less noisy. Here, we show that one can globally predict chromatin accessibility and infer regulatory element activities using RNA-seq. Genome-wide chromatin accessibility predicted by RNA-seq from 30 cells can offer better accuracy than ATAC-seq from 500 cells. Predictions based on single-cell RNA-seq (scRNA-seq) can more accurately reconstruct bulk chromatin accessibility than using scATAC-seq. Integrating ATAC-seq with predictions from RNA-seq increases the power and value of both methods. Thus, transcriptome-based prediction provides a new tool for decoding gene regulatory circuitry in samples with limited cell numbers.
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Benesova, Sarka, Mikael Kubista, and Lukas Valihrach. "Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis." Diagnostics 11, no. 6 (May 27, 2021): 964. http://dx.doi.org/10.3390/diagnostics11060964.

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MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol’s performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.
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Gupta, Vikas, Katharina Markmann, Christian N. S. Pedersen, Jens Stougaard, and Stig U. Andersen. "shortran: a pipeline for small RNA-seq data analysis." Bioinformatics 28, no. 20 (August 22, 2012): 2698–700. http://dx.doi.org/10.1093/bioinformatics/bts496.

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Nesline, Mary K., Sarabjot Pabla, Yong Hee Lee, Paul DePietro, Amy Early, Roger Klein, Shengle Zhang, and Jeffrey Conroy. "Abstract 1259: PD-L1 expression by RNA-sequencing and survival from pembrolizumab in non-small cell lung cancer (NSCLC)." Cancer Research 82, no. 12_Supplement (June 15, 2022): 1259. http://dx.doi.org/10.1158/1538-7445.am2022-1259.

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Abstract PURPOSE: The immunohistochemistry companion diagnostic test for pembrolizumab (IHC 22C3 pharmDx) lacks sensitivity, challenging immunotherapy selection for NSCLC patients with lower levels of expression. Unlike IHC 22C3, which restricts assessment of PD-L1 expression to viable tumor cells as a tumor proportion score (% TPS), mRNA next generation sequencing (RNA-seq) measures PD-L1 expression in the tumor microenvironment for both tumor and inflammatory background cells. RNA-seq previously demonstrated concordance with IHC and may be a robust alternative testing method for multiple tumor types. Here, we sought to optimize PD-L1 RNA-seq cutoff values in NSCLC to improve clinical sensitivity. PROCEDURE: NSCLC patients included in the study (n=3,465) were tested for PD-L1 expression by IHC 22C3 and clinically validated RNA-seq, measured as % rank (0-100) relative to a reference population based on normalized reads per million (nRPM). Patients were divided into an RNA-seq cut-off discovery cohort (n=3,168), and a test cohort pembrolizumab treated patients. Principal components analysis (PCA) was used to classify patients based on test results and explore cut-off values in the discovery cohort. Kaplan Meier curves and a Cox proportional hazards regression models assessed overall survival (OS) hazard ratios (HR) for RNA-seq versus standard of care IHC cut-offs in the test cohort. RESULTS: Unsupervised PCA clustering identified three distinct PD-L1 groups separated by combinations of significant over- and under-representation of RNA-seq and IHC result measures from prior testing. The groups were labeled as “low” (rank ≤40), “moderate” (rank 41-73), and “high” (rank ≥74), based on the median RNA-seq rank for each group (+/- 1SD for low and high). Both the low and moderate groups were overrepresented by patients in the PD-L1 IHC low and negative groups. The moderate group was overrepresented by patients with moderately high PD-L1 RNA-seq ranks (median=70), while the low group was overrepresented by patients that were not PD-L1 high by RNA-seq. The high group was overrepresented by patients high for PD-L1 by both IHC and RNA-seq. OS HRs were better for RNA-seq high versus moderate (HR=0.05, CI 0.00-0.63, p=.02), and RNA-seq high versus low (HR=0.16, CI 0.03-0.86, p=.03) groups compared to standard of care IHC 22C3 high versus low groups, (HR=0.21, CI 0.04-1.07, p=.06). Findings were non-significant for the RNA-seq moderate versus low groups, likely due to the limited and disproportionately high number of patients with poor performance status in these groups. CONCLUSIONS: PD-L1 expression by RNA-seq demonstrated improved clinical sensitivity in predicting OS versus standard of care PD-LI IHC in a pembrolizumab treated NSCLC patient cohort. Additional studies are needed to further define cut-offs in the context of performance status, and better understand immune escape mechanisms in the moderate group. Citation Format: Mary K. Nesline, Sarabjot Pabla, Yong Hee Lee, Paul DePietro, Amy Early, Roger Klein, Shengle Zhang, Jeffrey Conroy. PD-L1 expression by RNA-sequencing and survival from pembrolizumab in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1259.
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Li, Feng, Karolina Elżbieta Kaczor-Urbanowicz, Jie Sun, Blanca Majem, Hsien-Chun Lo, Yong Kim, Kikuye Koyano, et al. "Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing." Clinical Chemistry 64, no. 7 (July 1, 2018): 1085–95. http://dx.doi.org/10.1373/clinchem.2017.285072.

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Abstract BACKGROUND It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA. Given the laborious procedures needed for RNA-Seq library construction, sequencing, data storage, and data analysis, saliva-specific and optimized protocols are essential. METHODS We compared different RNA isolation methods and library construction kits for long and small RNA sequencing. The role of ribosomal RNA (rRNA) depletion also was evaluated. RESULTS The miRNeasy Micro Kit (Qiagen) showed the highest total RNA yield (70.8 ng/mL cell-free saliva) and best small RNA recovery, and the NEBNext library preparation kits resulted in the highest number of detected human genes [5649–6813 at 1 reads per kilobase RNA per million mapped (RPKM)] and small RNAs [482–696 microRNAs (miRNAs) and 190–214 other small RNAs]. The proportion of human RNA-Seq reads was much higher in rRNA-depleted saliva samples (41%) than in samples without rRNA depletion (14%). In addition, the transfer RNA (tRNA)-derived RNA fragments (tRFs), a novel class of small RNAs, were highly abundant in human saliva, specifically tRF-4 (4%) and tRF-5 (15.25%). CONCLUSIONS Our results may help in selection of the best adapted methods of RNA isolation and small and long RNA library constructions for salivary exRNA studies.
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Han, Bo W., Wei Wang, Phillip D. Zamore, and Zhiping Weng. "piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing." Bioinformatics 31, no. 4 (October 17, 2014): 593–95. http://dx.doi.org/10.1093/bioinformatics/btu647.

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Dissertations / Theses on the topic "Small RNA-Seq"

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Plakos, Kory. "Platinum-seq: High-throughput mapping of small-molecule platinum adducts on cellular RNA." Thesis, University of Oregon, 2017. http://hdl.handle.net/1794/22269.

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Methods to map small-molecule interactions with cellular RNAs are important for understanding endogenous activation, such as in riboswitches, as well as the potential for exogenous compounds to target RNA. Cisplatin is one of the most widely used of the platinum anticancer drugs that are prescribed in approximately 40-50% of all chemotherapy treatments (Dyson and Sava, 2006; Harper et al., 2010). Despite nearly 40 years of experience with this class of drugs, we still lack a comprehensive understanding of the targets of Pt compounds and their effects on cells. Pt(II) compounds are well-known DNA and RNA crosslinking agents, but the latter area is under-studied. In order to better understand the impacts of cisplatin and other platinum(II)-derived small molecules on cellular RNA, we have developed a technique we call “Platinum-seq,” which couples reverse transcription mapping of platinated RNAs to high-throughput sequencing. Chapter 1 is a study of cisplatin and a novel click-functionalized platinum compound (2-ADAP Pt) binding to the HDV ribozyme, a small catalytic RNA. Chapter 2 moves our platinum mapping approaches from low-throughput, sequencing gel based methods into next-generation sequencing for high-throughput analysis of all platinum sites in cellular RNA, a method we have named “Platinum-seq.” Chapter 3 is a study of differential gene expression of Saccharomyces cerevisiae treated with cisplatin and a second novel platinum(II) compound (azaplatin), using data acquired from the work in Chapter 2. Chapter 4 describes recent efforts to implement pre-enrichment of sequencing targets using click chemistry followed by DNA hybridization, in order to enrich for platinated fragments before sequencing library construction. Together, this work represents a significant step forward in advancing analysis of Pt(II) binding to cellular RNA, a potentially important target for this widely used class of anticancer compounds. Methods developed here are broadly applicable to genome-wide identification of platinum accumulation on DNA as well, which has not been pursued despite the extensive use of these compounds.
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Burr, Andrew John. "PISEQ ANALYIS IDENTIFIES NOVEL PIRNA IN SOMATIC CELLS THROUGH RNA-SEQ GUIDED FUNCTIONAL ANNOTATION AND GENOMIC ANALYSIS." Case Western Reserve University School of Graduate Studies / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=case1501150746104887.

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Reddy, Veena K. "Analysis of single cell RNA seq data to identify markers for subtyping of non-small cell lung cancer." Thesis, Högskolan i Skövde, Institutionen för biovetenskap, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-18514.

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Single cell RNA technology is a recent technical advancement used to understand the cancertumorgenicity at single cell resolution. In this study we have analyzed the scRNA data from thenon-small cell lung cancer (NSCLC) dataset to facilitate the early identification of NSCLCsubtypes namely, squamous cell carcinoma (SCC) and adenocarcinoma (AC). Non-immunecells, have a major role in tumorigenesis of the malignant tumors, in early stages. Therefore,we have analyzed the major non-immune cells, namely endothelial cells and fibroblast cellsfrom the GSE127465 dataset using SEURAT pipeline. Dimensionality reduction analysis andcluster analysis indicate that AC and SCC subtypes of NSCLC have different fibroblastcompositions. Differential gene expression analysis indicates that AC tumours have shownelevated content of MGP/PTGDS and INMT/MFAP4 fibroblast cells, whereas squamous cellcarcinoma showed an elevated content of COL6A1/COL6A2 and FNDC1/COL12A1 fibroblastcells. The statistical analysis shows that the clustering is statistically significant and not anartefact. Given that the tumour microenvironment is highly dynamic, in this study we haveattempted to understand the tumour microenvironment by scRNA analysis of non-immune cellsat single cell resolution.
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Santana, Estevan Alexis. "Identification of a Fur-regulated small regulatory RNA in nontypeable Haemophilus influenzae." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1410472201.

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Santos, Sara F. C. [Verfasser], Jörg [Gutachter] Vogel, Alexander J. [Gutachter] Westermann, and Jay [Gutachter] Hinton. "Expanding the targetome of Salmonella small RNA PinT using MS2 affinity purification and RNA-Seq (MAPS) / Sara F. C. Santos ; Gutachter: Jörg Vogel, Alexander J. Westermann, Jay Hinton." Würzburg : Universität Würzburg, 2021. http://d-nb.info/1238018351/34.

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Leonard, Simon. "Identification d'ARN régulateurs bactériens : développement d’une méthode de détection et étude de la régulation post-transcriptionnelle chez la bactérie phytopathogène Dickeya dadantii." Thesis, Lyon, 2018. http://www.theses.fr/2018LYSE1279.

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Les organismes bactériens sont en contact direct avec leur environnement et doivent donc constamment s’acclimater aux variations de celui-ci. Pour cela, plusieurs leviers de régulations peuvent être actionnés. Récemment, la régulation post-transcriptionnelle par les ARN régulateurs a été proposée comme un mécanisme de régulation rapide et peu coûteux pour la cellule. Chez le phytopathogène Dickeya dadantii, la régulation de la virulence a quasi exclusivement été étudiée au niveau transcriptionnel et l’implication des ARN régulateurs dans la virulence reste très peu connue. Pour cela, nous avons tout d’abord étudié le rôle des chaperons à ARN dans la pathogénie de D. dadantii et mis en évidence leur implication dans de nombreux facteurs de virulence comme la production d’enzyme de dégradation de la paroi végétale. Puis, nous avons développé une nouvelle méthode d’identification d’ARN à partir de données RNA-seq. Cette méthode a été développée pour tirer profit des séquençages réalisés en paired-end, permettant de séquencer les deux extrémités d’un transcrit. Son évaluation dans sa capacité à détecter de manière précise des ARN connus a montré une performance supérieure aux méthodes de détection existantes. Enfin, cette nouvelle méthode a été appliquée sur des données de séquençage de petits transcrits. Cette analyse nous a permis d’identifier plus d’un millier d’ARN régulateurs potentiels, dont plusieurs pourraient être impliqués dans la régulation de la virulence. Ces travaux ont donc permis de mettre en lumière l’existence d’une régulation post-transcriptionnelle chez D. dadantii et de proposer des pistes concernant les acteurs et mécanismes concernés
Bacterial organisms are directly exposed to environmental conditions and have to respond to environmental stress. To do so, several regulation network are known. Recently, post transcriptional regulation with small RNAs was suggested to be a fast and cheap in energy regulation mechanism. In the phytopathogen Dickeya dadantii, investigations on pathogenic process mostly focused on its control by transcriptional regulators. Knowledge of post-transcriptional regulation of the virulence factors is still in its infancy.To this end, we first studied the impact of RNA chaperones in the virulence of D. dadantii and showed that they were involved in the regulation of several virulence factors, like production of cell wall degrading enzyme. Then, we developed a new method to detect sRNAs from paired-end bacterial RNA-seq data. This method take paired end sequencing into account, which allow the sequencing of the both ends of each fragment. A comparative assessment showed that this method outperforms all the existing methods in terms of sRNA detection and boundary precision. Finally, this method was applied to sequencing data. With this analysis, more than one thousand sRNAs has been detected, with the identification of several candidates potentially involved in virulence.Thereby, this work highlight the existence of post-transcriptionnal regulation in D. dadantii and suggest candidates and mechanisms involved in this regulation
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Agirre, Ortiz de Guzmán Eneritz 1983. "Epigenetics in alternative splicing : links between chromatin structure, transcription and non-coding RNA mediated regulation." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/128682.

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Generalment s'ha pensat que la regulació de l'splicing alternatiu està controlada principalment per la interacció entre els factors reguladors de l'splicing i la taxa d'elongació de la ARN polimerasa II (RNAPII). Hi ha un evidencia emergent de la complexitat de la regulació de l'splicing alternatiu, que ara també inclou l'activitat d'ARNs no codificants i l'estat de la cromatina. Diverses experiments han demostrat que modificacions en les histones poden regular la inclusió d'exons alternatius, i que la taxa d'elongació de la RNAPII pot estar influenciada pels diferents estats de la cromatina. Els ARNs petits (sRNAs) són una família d'ARNs no codificants associats amb membres de la família de proteïnes Argonauta i són efectors de la via de silenciació gènica. Alguns sRNAs participen en una via alternativa anomenada via de silenciació gènica transcripcional (TGS). Evidències experimentals ha mostrat que els sRNAs interferents que s'uneixen a introns poden promoure l'aparició de modificacions en les histones que alteren la taxa de elongació de la transcripció provocant canvis en l'splicing alternatiu. Aquesta via és coneguda com via de silenciació gènica transcripcional acoplada a splicing alternatiu (TGS-AS). Tenint aixó en compte, nosaltres vam proposar que la proteïna Argonauta 1 (AGO1), podria induir la formació d'heterocromatina i canviar l'splicing alternatiu alterant l'elongació de la RNAPII. Per tal de realitzar una análisi a escala genómica de la regulació de l'splicing alternatiu, hem utilitzat dades provinents de noves tècniques de seqüenciació a gran escala, com ChIP-Seq i RNA-Seq. Hem trobat que hi ha regulació d'splicing alternatiu depenent d'AGO1. Els nostres resultats suggereixen que ARNs interferents endógens podrien estar relacionats amb aquesta regulació. A més, a la part final de la tesi demostrem que hi ha un codi de cromatina que requereix AGO1 que regula l'splicing alternatiu i que és específic per diferents tipus cel·lulars. Adicionalment hem trobat que altres efectors, com CTCF i HP1 alpha, també sòn importants per explicar els canvis en l'splicing dels pre-ARNs. Conjunatment amb altres treballs, aquesta tesis demostra que la regulació de l'splicing alternatiu implica la funció de molts components nuclears i probablement de molts altres que encara han de ser descoberts.
The regulation of alternative splicing has been generally thought of being primarily controlled by the interaction of splicing factors with the RNA molecule and by the elongation rate of the RNA polymerase II (RNAPII). There is an emerging understanding of the complexity of how alternative splicing is regulated which now involves the activity of non-coding RNAs and the chromatin state. Different experiments have shown that histone modifications can regulate the inclusion of alternative exons and that the elongation rate of the RNAPII could be influenced by different chromatin states. In this sense, small RNAs (sRNAs), which are a family of non-coding RNAs associated with members of the Argonaute family of proteins, that are effectors of the silencing pathway, which can participate in an alternative pathway known as transcriptional gene silencing (TGS). Experimental evidence shows that siRNAs targeting introns can induce chromatin marks that affect the rate of transcriptional elongation, affecting the splicing of pre-mRNAs, which is called transcriptional gene silencing alternative splicing (TGS-AS) \citep{Allo2009}. Thus, we proposed that the Argonaute protein (AGO1) could trigger heterochromatin formation and affect splicing by affecting RNAPII elongation. In order to perform a genome-wide analysis of the regulation of alternative splicing we used new highthroughput sequencing technologies as ChIP-Seq and RNA-Seq. We found that there is AGO1 dependent alternative splicing regulation, and our results suggest that endogenous sRNAs could be involved. Additionally, in the last part of the thesis we show a cell specific alternative splicing chromatin code, which also involves AGO1. Even though AGO1 regulation of alternative splicing was related to some specific cases, we found that other effectors, CTCF and HP1$\alpha$ were also important for the splicing changes decisions. This thesis and other recent reports show the regulation of alternative splicing as an integrated process,
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Souki, Rima. "Utilisation des miARN circulants comme indicateurs d'exposition aux hydrocarbures aromatiques polycycliques seuls et en mélange." Electronic Thesis or Diss., Université de Rennes (2023-....), 2023. http://www.theses.fr/2023URENB015.

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Les Hydrocarbures Aromatiques Polycycliques (HAP) sont des polluants environnementaux majeurs présentant des effets toxiques sur la santé humaine. Parmi les types cellulaires ciblés par les HAP, se trouvent les cellules mononucléaires circulantes du sang (PBMC). La présente étude vise à 1) étudier l'effet du B[a]P, HAP de référence, sur le profil d'expression des microARN (miRNA)in vitro dans les PBMC, ainsi que dans les vésicules extracellulaires (EV) sécrétées par ces cellules, en utilisant une approche de small RNA-seq, 2) Confirmer la présence de miRNA vésiculaires in vivo dans le plasma de rats traités par le B[a]P, 3) analyser, par une approche bioinformatique, les cibles potentielles des miRNA cellulaires et vésiculaires et caractériser, leurs voies de signalisation et fonctions biologiques et 4) comprendre le rôle des EV et de leurs miRNA sur la fonction et le phénotype des cellules endothéliales adjacentes. Nos résultats ont identifié les miARN régulés par le B[a]P dans les PBMCs et l'ontologie a montré que leurs gènes cibles étaient principalement impliqués dans les processus de mort et survie cellulaires. Des études plus approfondies ont révélé l’importance du miR-132, régulé par le B[a]P de manière dose- et temps-dépendants et qui nécessite l’activation du récepteur aryl hydrocarbon (AhR). Nous avons aussi démontré que ce miR-132 était impliqué dans la mort cellulaire induite par le B[a]P, en modifiant la balance des cytochromes P-450 (CYP) de la famille 1, classiquement régulés par l’AhR. Nos résultats rapportent ensuite une augmentation de la libération d'EV à la fois in vitro à partir de PBMC exposées et in vivo dans le plasma de rats exposés au B[a]P et proposent un panel de miRNA vésiculaires régulés par l'exposition aux HAP. Enfin, l'analyse ontologique a révélé différents profils d'expression de miRNA entre les PBMC et leurs EV, en lien avec un adressage sélectif des miRNA à l'intérieur des EV. Cette dernière analyse nous a conduit à nous intéresser au rôle des EV issues des PBMC après exposition aux HAP sur les cellules endothéliales voisines. Nos premiers résultats montrent une internalisation de ces EV associée à une modification de l’expression des gènes endothéliaux impliqués dans l'inflammation, le stress oxydatif et la migration. Au total, ces études proposent les EV et les miRNA comme de nouveaux outils non seulement pour étudier les mécanismes de toxicité des HAP mais aussi pour identifier des marqueurs d’exposition à ces polluants environnementaux
Polycyclic Aromatic Hydrocarbons (PAH) are major environmental pollutants with toxic effects on human health. Among the cell types targeted by PAHs are circulating blood mononuclear cells (PBMC). The present study aims to 1) investigate the effect of B[a]P, a reference PAH, on the expression profile of microRNAs (miRNAs) in vitro in PBMCs, as well as in extracellular vesicles (EVs) secreted by these cells, using a small RNA-seq approach, 2) confirm the presence of vesicular miRNAs in vivo in the plasma of B[a]P-treated rats, 3) to analyze, by a bioinformatics approach, the potential targets of cellular and vesicular miRNAs and characterize, their signaling pathways and biological functions and 4) to understand the role of EVs and their miRNAs on the function and phenotype of adjacent endothelial cells. Our results identified B[a]P regulated miRNAs in PBMCs and ontology showed that their target genes were mainly involved in cell death and survival processes. Further studies revealed the importance of miR-132, which is regulated by B[a]P in a dose- and time-dependent manner, and require activation of the aryl hydrocarbon receptor (AhR). We also demonstrated that this miR-132 was involved in B[a]P-induced cell death by altering the balance of family 1 cytochrome P-450 (CYP), classically regulated by AhR. Our results then report an increase in EV release both in vitro from exposed PBMCs and in vivo in plasma from B[a]P-exposed rats and propose a panel of vesicular miRNAs regulated by PAH exposure. Finally, the ontological analysis revealed different miRNA expression profiles between PBMCs and their EVs, related to selective miRNA addressing within EVs. This last analysis led us to investigate the role of EVs from PBMCs after exposure to PAHs on neighboring endothelial cells. Our first results show internalization of these EVs is associated with a modification of the expression of endothelial genes involved in inflammation, oxidative stress, and migration. Altogether, these studies propose EVs and miRNAs as new tools not only to study the mechanisms of PAH toxicity but also to identify markers of exposure to these environmental pollutants
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Klevebring, Daniel. "On Transcriptome Sequencing." Doctoral thesis, KTH, Genteknologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11446.

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This thesis is about the use of massive DNA sequencing to investigate the transcriptome. During recent decades, several studies have made it clear that the transcriptome comprises a more complex set of biochemical machinery than was previously believed. The majority of the genome can be expressed as transcripts; and overlapping and antisense transcription is widespread. New technologies for the interroga- tion of nucleic acids have made it possible to investigate such cellular phenomena in much greater detail than ever before. For each application, special requirements need to be met. The work presented in this thesis focuses on the transcrip- tome and the development of technology for its analysis. In paper I, we report our development of an automated approach for sample preparation. The procedure was benchmarked against a publicly available reference data set, and we note that our approach outperformed similar manual procedures in terms of reproducibility. In the work reported in papers II-IV, we used different massive sequencing technologies to investigate the transcriptome. In paper II we describe a concatemerization approach that increased throughput by 65% using 454 sequencing,and we identify classes of transcripts not previously described in Populus. Papers III and IV both report studies based on SOLiD sequencing. In the former, we investigated transcripts and proteins for 13% of the human gene and detected a massive overlap for the upper 50% transcriptional levels. In the work described in paper IV, we investigated transcription in non-genic regions of the genome and detected expression from a high number of previ- ously unknown loci.
QC 20100723
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Bovolenta, Luiz Augusto. "Análise exploratória em larga escala de microRNAs expressos em tilápia do Nilo utilizando ferramentas de bioinformática." Botucatu, 2016. http://hdl.handle.net/11449/148567.

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Orientador: Ney Lemke
Resumo: MicroRNAs (miRNAs) são pequenas moléculas de RNA que regulam pós-transcricionalmente a expressão de genes, modelando o transcriptoma e a produção de proteínas. Em geral, os miRNAs são conservados no genoma de eucariotos, sendo considerados elementos vitais em diversos processos biológicos durante o desenvolvimento, tais como crescimento, diferenciação e morte celular. A grande diversidade de miRNAs identificados está restrita a poucas espécies e apenas uma parte do total de alvos de miRNAs preditos foi caracterizada funcionalmente. Nesse contexto, o uso da tecnologia de sequenciamento de alto rendimento (high throughput sequencing) atrelada à análise de nível transcricional por RT-qPCR possibilitam a identificação do microRNoma. A tilápia do Nilo, Oreochromis niloticus, é considerada um excelente modelo biológico para o estudo de miRNAs em vertebrados devido à sua importância econômica e evolutiva. O presente trabalho teve como objetivos: organizar os dados do sequenciamento dos miRNAs da tilapia do Nilo; disponibilizá-los em forma de uma base de dados para a comunidade científica; integrar as informações dos miRNAs identificados com outros bancos de dados de miRNAs; analisar os dados através de análises de bioinformática para determinação de agrupamentos definidos pelo nível de expressão de cada miRNA em seis tipos de tecido (músculo branco, músculo vermelho, testículo, ovário, fígado, olho, cérebro e coração) com distinção entre os gêneros e nas fases do desenvolvimento (2,... (Resumo completo, clicar acesso eletrônico abaixo)
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Book chapters on the topic "Small RNA-Seq"

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Tai, Chin-Hsien, Deborah Hinton, and Sung-Huan Yu. "Discovering Novel Bacterial Small RNA by RNA-seq Analysis Toolkit ANNOgesic." In Methods in Molecular Biology, 35–69. New York, NY: Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-3565-0_4.

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Hrabeta-Robinson, Eva, Erin Marcus, Aaron E. Cozen, Eric M. Phizicky, and Todd M. Lowe. "High-Throughput Small RNA Sequencing Enhanced by AlkB-Facilitated RNA de-Methylation (ARM-Seq)." In Methods in Molecular Biology, 231–43. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6807-7_15.

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Wan, Xiangyuan, and Ziwen Li. "Computational Identification of ceRNA and Reconstruction of ceRNA Regulatory Network Based on RNA-seq and Small RNA-seq Data in Plants." In Modeling Transcriptional Regulation, 261–75. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1534-8_17.

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Shakola, Felitsiya, Valeriya Simeonova, and Ivan Ivanov. "Comparison of Four Classification Methods on Small-Sample-Size Synthetic RNA-seq Data." In Advanced Computing in Industrial Mathematics, 111–21. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-20951-2_11.

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Vans, Edwin, Alok Sharma, Ashwini Patil, Daichi Shigemizu, and Tatsuhiko Tsunoda. "Clustering of Small-Sample Single-Cell RNA-Seq Data via Feature Clustering and Selection." In PRICAI 2019: Trends in Artificial Intelligence, 445–56. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-29894-4_36.

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Arce, D. P., F. J. Krsticevic, M. R. Bertolaccini, J. Ezpeleta, S. D. Ponce, and E. Tapia. "Analysis of Small Heat Shock Protein Gene Family Expression (RNA-Seq) during the Tomato Fruit Maturation." In VI Latin American Congress on Biomedical Engineering CLAIB 2014, Paraná, Argentina 29, 30 & 31 October 2014, 679–82. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-13117-7_173.

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van Dijk, Erwin L., and Claude Thermes. "A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2′-O-Methyl RNAs." In Methods in Molecular Biology, 153–67. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1374-0_10.

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Sedlar, Karel, and Ralf Zimmer. "Comparison of Stranded and Non-stranded RNA-Seq in Predicting Small RNAs in a Non-model Bacterium." In Bioinformatics and Biomedical Engineering, 45–56. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-07802-6_4.

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Hamazaki, Nobuhiko, Kinichi Nakashima, Katsuhiko Hayashi, and Takuya Imamura. "Detection of Bidirectional Promoter-Derived lncRNAs from Small-Scale Samples Using Pre-Amplification-Free Directional RNA-seq Method." In Methods in Molecular Biology, 83–103. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6988-3_6.

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Carrillo-Perez, Francisco, Juan Carlos Morales, Daniel Castillo-Secilla, Alberto Guillen, Ignacio Rojas, and Luis Javier Herrera. "Comparison of Fusion Methodologies Using CNV and RNA-Seq for Cancer Classification: A Case Study on Non-Small-Cell Lung Cancer." In Bioengineering and Biomedical Signal and Image Processing, 339–49. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-88163-4_29.

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Conference papers on the topic "Small RNA-Seq"

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Koduru, Srinivas V., Angelique Nyinawabera, Dino J. Ravnic, and Amit K. Tiwari. "Abstract 3490: Interrogation of small RNA-seq data for small noncoding RNA in human colon cancer." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-3490.

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Kim, Hyunsoo, and Ramana V. Davuluri. "Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets." In the First ACM International Conference. New York, New York, USA: ACM Press, 2010. http://dx.doi.org/10.1145/1854776.1854871.

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Koduru, Srinivas V., and Dino J. Ravnic. "Abstract 3489: Noncoding RNA distribution in clear cell renal cell cancer: small RNA-seq data." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-3489.

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PEÑA-CASTILLO, LOURDES, MARC GRÜELL, MARTIN E. MULLIGAN, and ANDREW S. LANG. "DETECTION OF BACTERIAL SMALL TRANSCRIPTS FROM RNA-SEQ DATA: A COMPARATIVE ASSESSMENT." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2015. http://dx.doi.org/10.1142/9789814749411_0042.

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Dimitrakopoulos, Georgios Ν., Konstantinos Lazaros, Aristidis G. Vrahatis, Marios Krokidis, Konstantina Skolariki, Panagiotis Vlamos, and Themis Exarchos. "A Machine Learning approach combining omics data for Alzheimer’s Disease analysis." In 2nd International Conference on Chemo and Bioinformatics. Institute for Information Technologies, University of Kragujevac, 2023. http://dx.doi.org/10.46793/iccbi23.342d.

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Alzheimer’s disease (AD) is a complex neurological disorder whose underlying mechanisms remain elusive to this day. Molecular biology methodologies, especially techniques like single-cell RNA sequencing (scRNA-seq), offer unparalleled granularity in deciphering the disease’s cellular intricacies. However, despite the potential of scRNA-seq, comprehensive machine-learning analyses are yet to be fully harnessed. Emphasizing the multi-omics machine-learning-based approaches, which integrate diverse single-cell omics datasets, could highlight novel therapeutic targets and deepen our understanding of AD’s intricate nature. In this work, we propose a machine-learning-based method to embed gene expression into a protein interaction graph. Specifically, we model each interaction with a regression model on the participating genes and we use the R2 score as edge weight. Our aim is to detect parts of the PPI graph that differentiate between control and disease conditions. Application on a scRNA-seq AD dataset managed to identify interactions forming small subgraphs, which consisted of genes involved with biological processes related to neurons.
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Koduru, Srinivas V., Amit K. Tiwari, Sprague W. Hazard, Milind K. Mahajan, and Dino J. Ravnic. "Abstract 4447: Analysis of small RNA-seq data for differential expression of small noncoding RNAs in human colorectal cancer." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-4447.

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Eshun, Robert B., Md Khurram Monir Rabby, A. K. M. Kamrul Islam, and Marwan U. Bikdash. "Histological classification of non-small cell lung cancer with RNA-seq data using machine learning models." In BCB '21: 12th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3459930.3471168.

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Kim, Eunji, Ivan Ivanov, Jianping Hua, Robert S. Chapkin, and Edward R. Dougherty. "Model-based study of the Effectiveness of Reporting Lists of Small Feature Sets using RNA-Seq Data." In BCB '16: ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2975167.2985636.

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Ben Ali, Ferid, Sola Adeleke, and Iosif Mporas. "Graph Convolutional Networks based Non-Small Cell Lung Cancer Identification using RNA-seq Data from Blood Samples." In 2023 IEEE EMBS Special Topic Conference on Data Science and Engineering in Healthcare, Medicine and Biology. IEEE, 2023. http://dx.doi.org/10.1109/ieeeconf58974.2023.10404411.

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Huang, Y., T. Li, Z. Huang, W. Deng, S. Zheng, X. Guo, and Z. Huang. "THU0010 Altered mirnas profiles in plasma-derived exosome of patients with ankylosing spondylitis by small rna-seq analysis." In Annual European Congress of Rheumatology, 14–17 June, 2017. BMJ Publishing Group Ltd and European League Against Rheumatism, 2017. http://dx.doi.org/10.1136/annrheumdis-2017-eular.5637.

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