Gene Ontology based housekeeping gene selection for RNA-seq normalization
Keywords: Gene Ontology; RNA-seq; Housekeeping gene; Comparative genomics; Differential gene expression;
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Mitochondrial EF4 links respiratory dysfunction and cytoplasmic translation in Caenorhabditis elegans
Keywords: C. elegans; Caenorhabditis elegans; WT; wild-type; EF4; elongation factor 4; mtEF4; mitochondrial EF4; mtDNA; mitochondrial DNA; BP; base pairs; ETC; electron transport chain; mtEFTu, mtEFG1 and mtEFTs; mitochondrial elongation factor Tu, G1 and Ts; MMP;
Research ArticleIdentification of prognostic biomarkers in hepatitis B virus-related hepatocellular carcinoma and stratification by integrative multi-omics analysis
Keywords: HCC; hepatocellular carcinoma; SNP; single nucleotide polymorphism; HBV; hepatitis B virus; RNA-Seq; RNA sequencing; CNV; copy number variation; SV; structural variation; RFS; recurrence-free survival; OS; overall survival; TERT; telomerase reverse transc
Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig
Keywords: DEGs; differentially expressed genes; JNP; Jeju Native Pig; GO; gene ontology; NGS; next generation sequencing; PE; paired-ends; CASAVA-v1.7; Consensus Assessment of Sequence and Variation v 1.7; UCSC; University of California Santa Cruz; EASE; Expression
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation
Keywords: Apostichopus japonicus; RNA-seq; Respiratory tree; Aestivation; Differential gene expression;
Changes in transcript abundance for cuticular proteins and other genes three hours after a blood meal in Anopheles gambiae
Keywords: Blood feeding; RNA-seq; Illumina sequencing; Microarray; Cuticular proteins; Diurnal cyclesNBF, non-blood fed; BF3h, blood fed 3 h; CP, cuticular protein; RT-qPCR, reverse transcription quantitative PCR; FPKM, fragments per kilobase per million mapped rea
Transcriptome and exoproteome analysis of utilization of plant-derived biomass by Myceliophthora thermophila
Keywords: Myceliophthora thermophila; Biomass degradation; Carbohydrate-active enzymes; RNA-Seq; Mass spectrometry; GH; glycoside hydrolase; CE; carbohydrate esterase; PL; polysaccharide lyase; AA; auxiliary activity family; CAZymes; carbohydrate-active enzymes; HW
Fat depot-specific gene signature and ECM remodeling of Sca1high adipose-derived stem cells
Keywords: Adipocyte; ECM; Collagen; MMP; Adipose-derived stem cell; RNA-seq; Obesity;
Insights into the olfactory system of the ectoparasite Caligus rogercresseyi: Molecular characterization and gene transcription analysis of novel ionotropic receptors
Keywords: Olfactory receptor; Ionotropic receptor; Caligus rogercresseyi; RNA-seq
Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits
Keywords: Mango (Mangifera indica Linn.); Transcriptome; RNA-Seq; Proteomics; Mass spectrometry
Phenotypic, genomic, transcriptomic and proteomic changes in Bacillus cereus after a short-term space flight
Keywords: Bacillus cereus; Space flight; Phenotype; Next-generation; RNA-seq; iTRAQ
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism
Keywords: RNA-seq; Differential expression; Xenopus;
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis
Keywords: GR; glucose restriction; CR; caloric restriction; NGS; next generation sequencing; RNA-seq; RNA sequencing; GK; Glucokinase; GPI; Glucose phosphate isomerase; PFK; Phosphofructokinase; ALDO; Fructose-1,6-bisP aldolase; TPI; Triose-phosphate isomerase; GAP
RNA-sequencing reveals previously unannotated protein- and microRNA-coding genes expressed in aleurone cells of rice seeds
Keywords: Rice; Aleurone; Abscisic acid; Gibberellic acid; MicroRNA; RNA-seq;
RNA sequencing of microglia and monocyte-derived macrophages from mice with experimental autoimmune encephalomyelitis illustrates a changing phenotype with disease course
Keywords: EAE; Experimental autoimmune encephalomyelitis; RNA-Seq; RNA sequencing; MoDMs; Monocyte-derived macrophages; MiDMs; Microglia-derived macrophages; IFA; Incomplete Freud's adjuvant; MFI; Median fluorescence intensity; IPA; Ingenuity Pathway Analysis; PC
Gene expression profile analysis of Ligon lintless-1 (Li1) mutant reveals important genes and pathways in cotton leaf and fiber development
Keywords: ACO; 1-aminocyclopropane-1-carboxylic acid oxidase; ADNI1; adenine nucleotide transporter 1; ALDH; aldehyde dehydrogenase; AP2; AP2-EREBP transcription factors; AS1; ASYMMETRIC LEAVES1; AS2; ASYMMETRIC LEAVES2; ATSS3; Arabidopsis starch synthase 3; ATBFRU
High-throughput SNP discovery and transcriptome expression profiles from the salmon louse Caligus rogercresseyi (Copepoda: Caligidae)
Keywords: Caligus rogercresseyi; SNPs; RNA-seq; MiSeq; Sea lice
Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods
Keywords: Prrx1; Prrx2; Genome duplication; Ohnolog; RNA-Seq; Paired appendages; Fin/limb bud; Craniofacial;
Original researchComparative Transcriptomics of Early Meiosis in Arabidopsis and Maize
Keywords: Meiosis; Transcriptome; RNA-seq; Meiocytes; Arabidopsis; Maize;
Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq
Keywords: RNA-Seq; Retina; Choroid; RPE; Gene expression; Retinitis pigmentosa; Macular degeneration; Transcriptome;
Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells
Keywords: ChIP; chromatin immunoprecipitation; GAPDH; glyceraldehyde 3-phosphate dehydrogenase; GO; gene ontology; H3K27me3; histone 3 lysine 27 trimethyl; HNSCC; head and neck squamous cell carcinoma; HOX; homeobox; HPRT1; hypoxanthine phosphoribosyltransferase 1;
Gene expression associated with intersterility in Heterobasidion
Keywords: Heterobasidion occidentale; Heterobasidion irregulare; Intersterility; Mating; RNA-seq
Transcriptomic Response to Yersinia pestis: RIG-I Like Receptor Signaling Response Is Detrimental to the Host against Plague
Keywords: Yersinia pestis; Innate immunity; RIG-I-like receptor signaling; RNA-seq; Transcriptomic response
Combinational usage of next generation sequencing and qPCR for the analysis of tumor samples
Keywords: qPCR; Oncology; NGS; Next generation sequencing; RNA-Seq; CNV;
Strand-specific RNA sequencing uncovers chloroplast ribonuclease functions
Keywords: Chloroplast; RNA-Seq; PNPase; Ribonuclease; RNA maturation; tRNA;
Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq
Keywords: RNA-Seq; ncRNA; RNase III; Zinc fragmentation; Segmentation;
Identifying differentially spliced genes from two groups of RNA-seq samples
Keywords: DSG; differentially spliced gene; NB; negative binomial; IPV; isoform proportion vector; MSDR; mean sequencing depth ratio; RPKM; reads per kilobase per million reads; Alternative splicing; RNA-Seq; Negative binomial model; Differential splicing; Exon-cen
Creation of a high-amylose durum wheat through mutagenesis of starch synthase II (SSIIa)
Keywords: Starch; Amylose; Wheat; RNA-seq; FSP; flour swelling power; SGP; starch granule protein;
Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis
Keywords: Bovine digital dermatitis; RNA-Seq; Pathway analysis; α2-Macroglobulin-like 1; Keratin;
Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling
Keywords: Blastomyces dermatitidis; RNA-Seq; In vivo transcriptional profiling; Experimental murine infection;
The effects of MucR on expression of type IV secretion system, quorum sensing system and stress responses in Brucella melitensis
Keywords: Brucella melitensis; MucR; RNA-seq;
Oral cavity tumors in younger patients show a poor prognosis and do not contain viral RNA
Keywords: Oral cavity squamous cell carcinoma; RNA-Seq; Oncovirus;
Design, construction and characterisation of a synthetic promoter library for fine-tuned gene expression in actinomycetes
Keywords: Synthetic promoter; Actinomycetes; GusA; RppA; Transcriptomic analysis; RNA-Seq; Erme promoter;
RNA sequencing and transcriptomal analysis of human monocyte to macrophage differentiation
Keywords: MDP; dendritic cell progenitor; SAGE; serial analysis of gene expression; RNA-seq; Illumina mRNA sequencing; PBMCs; peripheral blood mononuclear cells; RPKM; reads per kilobase of exon model per million; DEGs; differentially expressed genes; KEGG; Kyoto E
Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq
Keywords: Fullerene; Next generation sequencing; Nanotoxicology; Gene expression; RNA-seq;
Predicting long non-coding RNAs using RNA sequencing
Keywords: Long non-coding RNA; RNA-seq; Next generation sequencing; lncRNAs;
RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei
Keywords: L. vannamei; RNA-Seq; Transcriptome; TSV infection; Disease resistance; Immune response;
Application of next generation qPCR and sequencing platforms to mRNA biomarker analysis
Keywords: Next generation sequencing; NGS; Digital PCR; mRNA biomarker; Nanofluidic PCR; RNA-Seq;
Opportunities and methods for studying alternative splicing in cancer with RNA-Seq
Keywords: RNA-Seq; Alternative splicing; Cancer; Transcriptomes; Bioinformatics;
An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function
Keywords: Transcriptome; RNA-seq; Noncoding RNA; GRO-seq; RNA-PET; CLIP-seq;
Proteomic analysis of sheep uterus reveals its role in prolificacy
Keywords: PG; polytocous group; MG; monotocous group; PF; polytocous of follicular phase; MF; monotocous of follicular phase; PL; polytocous of lutein phase; ML; monotocous of lutein phase; TMT; tandem mass tag; HPLC; high-performance liquid chromatography; PRM; pa
Arabidopsis chloroplast quantitative editotype
Keywords: RNA editing; Chloroplast; RNA-seq; PNPase; Pentatricopeptide repeat; RNA processing
Achieving high throughput sequencing of a cDNA library utilizing an alternative protocol for the bench top next-generation sequencing system
Keywords: RNA-Seq; Next-generation sequencing; GS Junior system
Transcriptome map of mouse isochores in embryonic and neonatal cortex
Keywords: Base composition; Isochores; GC level; RNA-seq; Expression; Developmental process
Alternative strategies for development of a reference transcriptome for quantification of allele specific expression in organisms having sparse genomic resources
Keywords: RNA-Seq; Transcriptome; Assembly; Read mapping; Allele specific; Interspecies hybrid
Human housekeeping genes, revisited
Keywords: housekeeping genes; RNA-seq; gene expression patterns; internal control; next generation sequencing
Complete mitochondrial genome of Concholepas concholepas inferred by 454 pyrosequencing and mtDNA expression in two mollusc populations
Keywords: Mitochondrial genome; Concholepas concholepas; RNA-Seq; Gene expression
PROGRESSION OF ‘OMICS’ METHODOLOGIES FOR UNDERSTANDING THE PATHOGENICITY OF CORYNEBACTERIUM PSEUDOTUBERCULOSIS: THE BRAZILIAN EXPERIENCE
Keywords: Corynebacterium pseudotuberculosis; SOLiD next generation sequencing; Ion Torrent next generation sequencing; SDS-PAGE; mass spectrometry; RNA-seq
Identification of immune-related SNPs in the transcriptome of Mytilus chilensis through high-throughput sequencing
Keywords: SNPs; Mytilus chilensis; Immunogenomics; RNA-seq;
Enriching pathogen transcripts from infected samples: A capture-based approach to enhanced host–pathogen RNA sequencing
Keywords: Capture; RNA-Seq; Transcript enrichment; Next-generation sequencing; Rift Valley fever virus; Francisella tularensis