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Repetitive element transcript accumulation is associated with inflammaging in humans
Chronic, low-grade inflammation increases with aging, contributing to functional declines and diseases that reduce healthspan. Growing evidence...
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SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy...
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Bookend: precise transcript reconstruction with end-guided assembly
We developed Bookend, a package for transcript assembly that incorporates data from different RNA-seq techniques, with a focus on identifying and...
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Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing
We developed a single-cell approach to detect CRISPR-modified mRNA transcript structures. This method assesses how genetic variants at splicing sites...
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Possible Contribution of Alternative Transcript Isoforms in Mature Biofilm Growth Phase of Candida glabrata
Expression of genome-wide alternative transcript isoforms and differential transcript isoform usage in different biological conditions (isoform...
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CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion
BackgroundRecent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins...
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The transposable element-derived transcript of LIN28B has a placental origin and is not specific to tumours
Transposable elements (TEs) are genetic elements that have evolved as crucial regulators of human development and cancer, functioning as both genes...
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Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq
RNA-seq has been used extensively to study expression responses to polyploidy. Most current methods for normalizing RNA-seq data yield estimates of...
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Myoglobin expression by alternative transcript in different mesenchymal stem cells compartments
BackgroundThe metabolic phenotype of stem cells is increasingly recognized as a hallmark of their pluripotency with mitochondrial and oxygen-related...
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Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability
BackgroundTranscription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the...
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Exploring Circular RNA Profile and Expression in Extracellular Vesicles
Extracellular vesicles (EVs) are small vesicles secreted by various cell types and are enriched in multiple body fluids. EVs containing RNA have the...
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Nascent Transcript Sequencing for the Map** of Promoters in Arabidopsis thaliana Mitochondria
Knowledge of mitochondrial transcription start sites and promoter sequences is key to understanding mechanisms of transcription initiation in plant...
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A germline chimeric KANK1-DMRT1 transcript derived from a complex structural variant is associated with a congenital heart defect segregating across five generations
Structural variants (SVs) pose a challenge to detect and interpret, but their study provides novel biological insights and molecular diagnosis...
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Transcript profiling of glutathione metabolizing genes reveals abiotic stress and glutathione-specific alteration in Arabidopsis and rice
Homoeostasis of glutathione (GSH) is crucial for plant survival and adaptability against stress. Despite the presence of complete Arabidopsis and...
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3′-tRF-CysGCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways
tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the...
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Ascorbate and Hydrogen Peroxide Modify Metabolite Profile of Wheat Differently
Effects of ascorbate (ASA) and hydrogen peroxide (H 2 O 2 ) on metabolite profile was compared in wheat. Interestingly, the redox environment became more...
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Sorting and packaging of RNA into extracellular vesicles shape intracellular transcript levels
BackgroundExtracellular vesicles (EVs) are released by nearly every cell type and have attracted much attention for their ability to transfer protein...
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The long transcript of lncRNA TMPO-AS1 promotes bone metastases of prostate cancer by regulating the CSNK2A1/DDX3X complex in Wnt/β-catenin signaling
The second most common male cancer is prostate cancer (PCa), which has a high tendency for bone metastasis. Long non-coding RNAs, including TMPO-AS1 ,...
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Transcript mining using fuzzy rough set theory in Oryza sativa grown under N-limited condition
In rice cultivation, crop yield and productivity rely on the efficient supply of nitrogen. Mismanagement of nitrogen, such as insufficient and...
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Aldehyde dehydrogenase superfamily in sorghum: genome-wide identification, evolution, and transcript profiling during development stages and stress conditions
BackgroundAldehyde dehydrogenases (ALDHs) are a family of NAD(P) + dependent enzymes that detoxify aldehydes by promoting their oxidation to...
