当前位置： SCI文献检索 > Scientific Reports期刊下所有文献 > Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.

Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data.

Abstract：

:RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at accurately quantifying gene expression levels from RNA-sequencing reads. We performed an independent benchmarking study using RNA-sequencing data from the well established MAQCA and MAQCB reference samples. RNA-sequencing reads were processed using five workflows (Tophat-HTSeq, Tophat-Cufflinks, STAR-HTSeq, Kallisto and Salmon) and resulting gene expression measurements were compared to expression data generated by wet-lab validated qPCR assays for all protein coding genes. All methods showed high gene expression correlations with qPCR data. When comparing gene expression fold changes between MAQCA and MAQCB samples, about 85% of the genes showed consistent results between RNA-sequencing and qPCR data. Of note, each method revealed a small but specific gene set with inconsistent expression measurements. A significant proportion of these method-specific inconsistent genes were reproducibly identified in independent datasets. These genes were typically smaller, had fewer exons, and were lower expressed compared to genes with consistent expression measurements. We propose that careful validation is warranted when evaluating RNA-seq based expression profiles for this specific gene set.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Everaert C,Luypaert M,Maag JLV,Cheng QX,Dinger ME,Hellemans J,Mestdagh P

doi

10.1038/s41598-017-01617-3

subject

Has Abstract

pub_date

2017-05-08 00:00:00

pages

1559

issue

1

issn

2045-2322

pii

10.1038/s41598-017-01617-3

journal_volume

7

pub_type

杂志文章

相关文献

Scientific Reports文献大全
  • The anti-tumor diterpene oridonin is a direct inhibitor of Nucleolin in cancer cells.

    abstract：:The bioactive plant diterpene oridonin displays important pharmacological activities and is widely used in traditional Chinese medicine; however, its molecular mechanism of action is still incompletely described. In vitro and in vivo data have demonstrated anti-tumor activity of oridonin and its ability to interfere w...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-35088-x

    authors： Vasaturo M,Cotugno R,Fiengo L,Vinegoni C,Dal Piaz F,De Tommasi N

    更新日期：2018-11-13 00:00:00

  • Improvement of Terahertz Wave Radiation for InAs Nanowires by Simple Dipping into Tap Water.

    abstract：:We report improvement of terahertz (THz) wave radiation for Si-based catalyst-free InAs nanowires (NWs) by simple dipping into tap water (DTW). In addition, the possibility of using InAs NWs as a cost-effective method for biomedical applications is discussed by comparison to bulk InAs. The peak-to-peak current signals...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep36094

    authors： Park DW,Bin Ji Y,Hwang J,Lee CR,Lee SJ,Kim JO,Noh SK,Oh SJ,Kim SH,Jeon TI,Jeong KU,Kim JS

    更新日期：2016-10-26 00:00:00

  • Enhancing elevated temperature strength of copper containing aluminium alloys by forming L12 Al3Zr precipitates and nucleating θ″ precipitates on them.

    abstract：:Strengthening by precipitation of second phase is the guiding principle for the development of a host of high strength structural alloys, in particular, aluminium alloys for transportation sector. Higher efficiency and lower emission demands use of alloys at higher operating temperatures (200 °C-250 °C) and stresses, ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-11540-2

    authors： Kumar Makineni S,Sugathan S,Meher S,Banerjee R,Bhattacharya S,Kumar S,Chattopadhyay K

    更新日期：2017-09-11 00:00:00

  • Synchronous primary esophageal squamous cell carcinoma and gastric adenocarcinoma: analysis of 41 cases treated in a single institution.

    abstract：:The present study investigated the treatment and survival outcomes of patients with synchronous primary esophageal squamous cell carcinoma and gastric adenocarcinoma. The medical records of 10,783 patients with primary esophageal squamous cancer treated at our institution between 1995 and 2012 were retrospectively rev...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep13335

    authors： Li X,Lin S,Zhang Y,Wang H

    更新日期：2015-08-20 00:00:00

  • Neural oscillations associated with auditory duration maintenance in working memory.

    abstract：:The neural representation of auditory duration remains unknown. Here, we used electroencephalogram (EEG) recordings to investigate neural oscillations during the maintenance of auditory duration in working memory (WM). EEG analyses indicated that the auditory duration length was not associated with changes in the thet...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-06078-2

    authors： Yu X,Chen Y,Qiu J,Li X,Huang X

    更新日期：2017-07-18 00:00:00

  • Cortico-subcortical metabolic correlates of olfactory processing in healthy resting subjects.

    abstract：:A wide network of interconnected areas was previously found in neuroimaging studies involving normal as well as pathological subjects; however literature seems to suffer from a lack of investigation in glucose metabolism behaviour under olfactory condition. Thus, the present work describe for the first time a pure olf...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep05146

    authors： Alessandrini M,Micarelli A,Chiaravalloti A,Candidi M,Bruno E,Di Pietro B,Schillaci O,Pagani M

    更新日期：2014-06-03 00:00:00

  • Consistent responses of the microbial community structure to organic farming along the middle and lower reaches of the Yangtze River.

    abstract：:Soil microorganisms play a crucial role in the biogeochemical cycling of nutrient elements and maintaining soil health. We aimed to investigate the response of bacteria communities to organic farming over different crops (rice, tea and vegetable) along the middle and lower reaches of the Yangtze River of China. Compar...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep35046

    authors： Wang W,Wang H,Feng Y,Wang L,Xiao X,Xi Y,Luo X,Sun R,Ye X,Huang Y,Zhang Z,Cui Z

    更新日期：2016-10-11 00:00:00

  • Capillary isoelectric focusing after sample enrichment with immunoaffinity chromatography in a single capillary.

    abstract：:For accurate micro-scale quantification of a specific protein in biological fluids, immunoaffinity chromatography (IAC) and isoelectric focusing (IEF) were combined in a single fused-silica capillary. The inner wall of the capillary was coated with an anti-E-tag antibody at the inlet side to form an IAC column, and po...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep39221

    authors： Shimura K,Nagai T

    更新日期：2016-12-15 00:00:00

  • A proteomic analysis of an in vitro knock-out of miR-200c.

    abstract：:Loss of miR-200c is correlated to advanced cancer-subtypes due to increased EMT and decreased treatment efficacy by chemotherapeutics. As miRNAs regulate a multitude of targets, the analysis of differentially expressed proteins upon a genomic knock-out (KO) is of interest. In this study, we generated a TALENs KO of mi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-25240-y

    authors： Ljepoja B,García-Roman J,Sommer AK,Fröhlich T,Arnold GJ,Wagner E,Roidl A

    更新日期：2018-05-02 00:00:00

  • Copper nanoparticles on controlled pore glass (CPG) as highly efficient heterogeneous catalysts for "click reactions".

    abstract：:We herein report that supported copper nanoparticles (CuNPs) on commercially available controlled pore glass (CPG), which exhibit high mechanical, thermal and chemical stability as compared to other silica-based materials, serve as a useful heterogeneous catalyst system for 1,3-dipolar cycloadditions ("click" reaction...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-77629-3

    authors： Rafi AA,Ibrahem I,Córdova A

    更新日期：2020-11-25 00:00:00

  • Protein-Protein Affinity Determination by Quantitative FRET Quenching.

    abstract：:The molecular dissociation constant, Kd, is a well-established parameter to quantitate the affinity of protein-protein or other molecular interactions. Recently, we reported the theoretical basis and experimental procedure for Kd determination using a quantitative FRET method. Here we report a new development of Kd de...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-35535-9

    authors： Jiang L,Xiong Z,Song Y,Lu Y,Chen Y,Schultz JS,Li J,Liao J

    更新日期：2019-02-14 00:00:00

  • Terrestrial mammalian wildlife responses to Unmanned Aerial Systems approaches.

    abstract：:Unmanned Aerial Systems (UAS) are increasingly being used recreationally, commercially and for wildlife research, but very few studies have quantified terrestrial mammalian reactions to UAS approaches. We used two Vertical Take-off and Landing (VTOL) UAS to approach seven herbivore species in the Moremi Game Reserve, ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-38610-x

    authors： Bennitt E,Bartlam-Brooks HLA,Hubel TY,Wilson AM

    更新日期：2019-02-14 00:00:00

  • Optimization of a MT1-MMP-targeting Peptide and Its Application in Near-infrared Fluorescence Tumor Imaging.

    abstract：:Membrane type 1 metalloproteinase (MT1-MMP) is an important regulator of cancer invasion, growth and angiogenesis, thus making it an attractive target for cancer imaging and therapy. A non-substrate peptide (MT1-AF7p) that bonded to the "MT-Loop" region of MT1-MMP was identified by using a phage-displayed peptide libr...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-28493-9

    authors： Ren L,Wang Y,Zhu L,Shen L,Zhang J,Wang J,Li H,Zheng Q,Yu D,Fang X

    更新日期：2018-07-09 00:00:00

  • Mindfulness-Based Stress Reduction (MBSR) or Psychoeducation for the Reduction of Menopausal Symptoms: A Randomized, Controlled Clinical Trial.

    abstract：:Psychological and behavioural interventions may be effective in reducing menopause-related symptoms. This randomized controlled trial aimed to evaluate the effectiveness of Mindfulness-based Stress Reduction (MBSR) in reducing menopause-related symptoms by comparing with an active control group, the menopause educatio...

    journal_title：Scientific reports

    pub_type： 临床试验,杂志文章,随机对照试验

    doi：10.1038/s41598-018-24945-4

    authors： Wong C,Yip BH,Gao T,Lam KYY,Woo DMS,Yip ALK,Chin CY,Tang WPY,Choy MMT,Tsang KWK,Ho SC,Ma HSW,Wong SYS

    更新日期：2018-04-26 00:00:00

  • Combination of Platelet expression of PKCepsilon and cardiac troponin-I for early diagnosis of chest pain patients in the emergency department.

    abstract：:A rapid differential diagnosis of the clinical conditions underlying chest pain is a relevant clinical issue. Specifically, a fast rule-in or -out of acute myocardial infarction (AMI) is mandatory to improve diagnostic outcome and cost-effectiveness of patient management. We demonstrated that Protein Kinase C (PKC) ep...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-38624-5

    authors： Carubbi C,Masselli E,Pozzi G,Mattioli M,Martini S,Goldoni M,Aloe R,Cervellin G,Vitale M,Gobbi G

    更新日期：2019-02-14 00:00:00

  • First exploration of radiation temperatures of the laser spot, re-emitting wall and entire hohlraum drive source.

    abstract：:This study explores the radiation field temperatures introduced by the laser spot, the re-emitting wall in a hohlraum and the entire hohlraum drive source. This investigation, which is the first of its kind, is based on the radiation fluxes from the laser spot and the re-emitting wall, which have been accurately measu...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-41424-6

    authors： Ren K,Liu S,Xie X,Du H,Hou L,Jing L,Yang D,Zhao Y,Yan J,Yang Z,Li Z,Dong J,Yang G,Li S,Cao Z,Lan K,Huo W,Liu J,Ren G,Ding Y,Jiang S

    更新日期：2019-03-25 00:00:00

  • Local management and landscape structure determine the assemblage patterns of spiders in vegetable fields.

    abstract：:Both field- and landscape-scale factors can influence the predator communities of agricultural pests, but the relative importance and interactions between these scales are poorly understood. Focusing on spiders, an important taxon for providing biological control, we tested the influence of field- and landscape-scale ...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-71888-w

    authors： Saqib HSA,Chen J,Chen W,Pozsgai G,Akutse KS,Ashraf MF,You M,Gurr GM

    更新日期：2020-09-15 00:00:00

  • Intrinsic temperature-dependent evolutions in the electron-boson spectral density obtained from optical data.

    abstract：:We investigate temperature smearing effects on the electron-boson spectral density function (I(2)χ(ω)) obtained from optical data using a maximum entropy inversion method. We start with two simple model input I(2)χ(ω), calculate the optical scattering rates at selected temperatures using the model input spectral densi...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep23647

    authors： Hwang J

    更新日期：2016-03-31 00:00:00

  • Nedd4-2 haploinsufficiency causes hyperactivity and increased sensitivity to inflammatory stimuli.

    abstract：:Nedd4-2 (NEDD4L in humans) is a ubiquitin protein ligase best known for its role in regulating ion channel internalization and turnover. Nedd4-2 deletion in mice causes perinatal lethality associated with increased epithelial sodium channel (ENaC) expression in lung and kidney. Abundant data suggest that Nedd4-2 plays...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep32957

    authors： Yanpallewar S,Wang T,Koh DC,Quarta E,Fulgenzi G,Tessarollo L

    更新日期：2016-09-08 00:00:00

  • Characterization of Chinese liquor aroma components during aging process and liquor age discrimination using gas chromatography combined with multivariable statistics.

    abstract：:Chinese liquor aroma components were characterized during the aging process using gas chromatography (GC). Principal component and cluster analysis (PCA, CA) were used to discriminate the Chinese liquor age which has a great economic value. Of a total of 21 major aroma components identified and quantified, 13 componen...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep39671

    authors： Xu ML,Yu Y,Ramaswamy HS,Zhu SM

    更新日期：2017-01-06 00:00:00

  • Designing new strategy for controlling DNA orientation in biosensors.

    abstract：:Orientation controllable DNA biosensors hold great application potentials in recognizing small molecules and detecting DNA hybridization. Though electric field is usually used to control the orientation of DNA molecules, it is also of great importance and significance to seek for other triggered methods to control the...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep14415

    authors： Feng C,Ding HM,Ren CL,Ma YQ

    更新日期：2015-09-24 00:00:00

  • Nicotine absorption from electronic cigarette use: comparison between experienced consumers (vapers) and naïve users (smokers).

    abstract：:Electronic cigarettes (ECs) are nicotine delivery devices that are proposed as tobacco harm reduction products to smokers. Nicotine delivery from ECs is potentially important in their efficacy as smoking substitutes. Herein, nicotine delivery from using a new-generation EC device (variable-wattage, set at 9 W) was eva...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep11269

    authors： Farsalinos KE,Spyrou A,Stefopoulos C,Tsimopoulou K,Kourkoveli P,Tsiapras D,Kyrzopoulos S,Poulas K,Voudris V

    更新日期：2015-06-17 00:00:00

  • Effect of acoustic standing waves on cellular viability and metabolic activity.

    abstract：:Acoustic standing wave devices offer excellent potential applications in biological sciences for drug delivery, cell manipulation and tissue engineering. However, concerns have been raised about possible destructive effects on cells due to the applied acoustic field, in addition to other produced secondary factors. He...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-65241-4

    authors： Levario-Diaz V,Bhaskar P,Carmen Galan M,Barnes AC

    更新日期：2020-05-22 00:00:00

  • Crotoxin promotes macrophage reprogramming towards an antiangiogenic phenotype.

    abstract：:Crotoxin (CTX) is the primary toxin of South American rattlesnake Crotalus durissus terrificus venom. CTX reduces tumour mass, and tumour cell proliferation and these effects seem to involve the formation of new vessels. Angiogenesis has a key role in tumour growth and progression and is regulated by macrophage secret...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-019-40903-0

    authors： de Araújo Pimenta L,de Almeida MES,Bretones ML,Cirillo MC,Curi R,Sampaio SC

    更新日期：2019-03-12 00:00:00

  • Optimization of human mesenchymal stem cell manufacturing: the effects of animal/xeno-free media.

    abstract：:Due to their immunosuppressive properties, mesenchymal stem cells (MSC) have been evaluated for the treatment of immunological diseases. However, the animal-derived growth supplements utilized for MSC manufacturing may lead to clinical complications. Characterization of alternative media formulations is imperative for...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep16570

    authors： Oikonomopoulos A,van Deen WK,Manansala AR,Lacey PN,Tomakili TA,Ziman A,Hommes DW

    更新日期：2015-11-13 00:00:00

  • Wet tropical climate in SE Tibet during the Late Eocene.

    abstract：:Cenozoic climate cooling at the advent of the Eocene-Oligocene transition (EOT), ~33.7 Ma ago, was stamped in the ocean by a series of climatic events albeit the impact of this global climatic transition on terrestrial environments is still fragmentary. Yet archival constraints on Late Eocene atmospheric circulation a...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-017-07766-9

    authors： Sorrel P,Eymard I,Leloup PH,Maheo G,Olivier N,Sterb M,Gourbet L,Wang G,Jing W,Lu H,Li H,Yadong X,Zhang K,Cao K,Chevalier ML,Replumaz A

    更新日期：2017-08-10 00:00:00

  • Group A Streptococcus establishes pharynx infection by degrading the deoxyribonucleic acid of neutrophil extracellular traps.

    abstract：:Group A Streptococcus (GAS) secretes deoxyribonucleases and evades neutrophil extracellular killing by degrading neutrophil extracellular traps (NETs). However, limited information is currently available on the interaction between GAS and NETs in the pathogenicity of GAS pharyngitis. In this study, we modified a mouse...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-020-60306-w

    authors： Tanaka M,Kinoshita-Daitoku R,Kiga K,Sanada T,Zhu B,Okano T,Aikawa C,Iida T,Ogura Y,Hayashi T,Okubo K,Kurosawa M,Hirahashi J,Suzuki T,Nakagawa I,Nangaku M,Mimuro H

    更新日期：2020-02-24 00:00:00

  • A microfluidic device for isolating intact chromosomes from single mammalian cells and probing their folding stability by controlling solution conditions.

    abstract：:Chromatin folding shows spatio-temporal fluctuations in living undifferentiated cells, but fixed spatial heterogeneity in differentiated cells. However, little is known about variation in folding stability along the chromatin fibres during differentiation. In addition, effective methods to investigate folding stabilit...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/s41598-018-31975-5

    authors： Takahashi T,Okeyo KO,Ueda J,Yamagata K,Washizu M,Oana H

    更新日期：2018-09-12 00:00:00

  • Interleukin-6 disrupts blood-testis barrier through inhibiting protein degradation or activating phosphorylated ERK in Sertoli cells.

    abstract：:It has been recently ascribed to several inflammatory cytokines (i.e. TGF-β3, TNF-α, and IL-1) a functional role in regulating Sertoli cell blood-testis barrier (BTB) dynamics. In the testis, IL-6 inhibits meiotic DNA synthesis during the seminiferous epithelium cycle, reduces sperm motility and influences the secreti...

    journal_title：Scientific reports

    pub_type： 杂志文章

    doi：10.1038/srep04260

    authors： Zhang H,Yin Y,Wang G,Liu Z,Liu L,Sun F

    更新日期：2014-03-03 00:00:00

  • Author Correction: The impact of the introduction of new recognition criteria for overwork-related cardiovascular and cerebrovascular diseases: a cross-country comparison.

    abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...

    journal_title：Scientific reports

    pub_type： 已发布勘误

    doi：10.1038/s41598-018-23047-5

    authors： Lin RT,Lin CK,Christiani DC,Kawachi I,Cheng Y,Verguet S,Jong S

    更新日期：2018-03-12 00:00:00