RNA
View article: Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs
Alzheimer's disease-induced phagocytic microglia express specific profile of coding and non-coding RNAs Open
This repository contains the data and the code used in Flavia's project. A folder can contain the starting raw data in "data", the R scripts in order of execution (op1, op2 ..) and the "output" folder that contains the final processed data…
View article: Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation
Single-cell data: Antigen-reactive CD4 T cells after SARS-CoV-2 vaccination show divergent phenotypic states with or without restimulation Open
Understanding T cell fate requires precise knowledge of antigen reactivity. For CD4+ T cells, conventional identification of antigen reactivity by peptide restimulation relies on cellular activation, but thereby also introduces…
View article: Unfolded protein response in endoplasmic reticulum stress associated with retinal degenerative diseases: A promising therapeutic target.
Unfolded protein response in endoplasmic reticulum stress associated with retinal degenerative diseases: A promising therapeutic target. Open
The unfolded protein response is a cellular pathway activated to maintain proteostasis and prevent cell death when the endoplasmic reticulum is overwhelmed by unfolded proteins. However, if the unfolded protein response fails to restore en…
View article: Conserved nsp3 TM2–Y Region in Nidoviruses / MD results
Conserved nsp3 TM2–Y Region in Nidoviruses / MD results Open
Positive-strand RNA viruses remodel host intracellular membranes to form replication organelles in cytoplasm. SARS-CoV-2 and other coronaviruses, which belong to Nidovirales order, replicate within double-membrane vesicles (DMVs) derived f…
View article: Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type
Mapping single cell eQTLs by using MatrixEQTL with pseudo-bulk cell type Open
These scripts are implementing a two-step approach for detecting eQTL and conditional eQTL analysis for cell type gene expression in single cell RNA seq study. Relevant R packages: SVA (version 3.52.0, DOI: 10.18129/B9.bioc.sva), MatrixEQT…
View article: Virtual screening, molecular docking, and molecular dynamics simulation reveal new insights into RNA polymerase inhibition for anti-tuberculosis drug discovery.
Virtual screening, molecular docking, and molecular dynamics simulation reveal new insights into RNA polymerase inhibition for anti-tuberculosis drug discovery. Open
This study highlights the effectiveness of combining virtual screening, molecular docking, MD simulations, and MM-PBSA analysis in identifying promising RNAP inhibitors. The results establish a strong foundation for further experimental va…
View article: Supplementary Table 1 from A Bispecific METxMET Antibody–Drug Conjugate with Cleavable Linker Is Processed in Recycling and Late Endosomes
Supplementary Table 1 from A Bispecific METxMET Antibody–Drug Conjugate with Cleavable Linker Is Processed in Recycling and Late Endosomes Open
CRISPR RNA gene list
View article: Supplementary Table 1 from Absence of Either <i>Ripk3</i> or <i>Mlkl</i> Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Supplementary Table 1 from Absence of Either <i>Ripk3</i> or <i>Mlkl</i> Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis Open
List of Differentially Expressed Genes from RNA Seq analysis
View article: Figure S3 from T Cell–intrinsic Immunomodulatory Effects of TAK-981 (Subasumstat), a SUMO-activating Enzyme Inhibitor, in Chronic Lymphocytic Leukemia
Figure S3 from T Cell–intrinsic Immunomodulatory Effects of TAK-981 (Subasumstat), a SUMO-activating Enzyme Inhibitor, in Chronic Lymphocytic Leukemia Open
Figure S3 shows Hallmark enrichment plot of RNA collected from naïve T cells from patients with CLL treated with TAK-981
View article: Development of an RT-LAMP−CRISPR/Cas12a assay for rapid and specific detection of Bandavirus dabieense
Development of an RT-LAMP−CRISPR/Cas12a assay for rapid and specific detection of Bandavirus dabieense Open
Bandavirus dabieense, a single-stranded RNA virus, is the causative agent of severe fever with thrombocytopenia syndrome (SFTS), a disease associated with high fatality rates. Early and accurate diagnosis is essential for improving clinica…
View article: Supplementary Data for: Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata
Supplementary Data for: Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata Open
This dataset accompanies the manuscript “Scalp Tape-Strip RNA Sequencing Captures Disease and Treatment-Responsive Signatures in Alopecia Areata”. It provides the processed transcriptomic data and analysis scripts used to characterize the …
View article: Supplementary Table 2 from Absence of Either <i>Ripk3</i> or <i>Mlkl</i> Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis
Supplementary Table 2 from Absence of Either <i>Ripk3</i> or <i>Mlkl</i> Reduces Incidence of Hepatocellular Carcinoma Independent of Liver Fibrosis Open
List of significantly altered transcripts from RNA Seq analysis
View article: Supplementary Tables and Figures from Triple-Negative Breast Cancer-Derived Extracellular Vesicles Promote a Hepatic Premetastatic Niche via a Cascade of Microenvironment Remodeling
Supplementary Tables and Figures from Triple-Negative Breast Cancer-Derived Extracellular Vesicles Promote a Hepatic Premetastatic Niche via a Cascade of Microenvironment Remodeling Open
Supplementary Table 1. Information about patients derived xenograft models and derived patient.Supplementary Table 2. Ontology of differentially expressed genes in metastasis-harboring liver of PDX models.Supplementary Table 3. Differentia…
View article: The sRNA for pollen development in Ogura-CMS Chinese Cabbage(Brassica rapa)
The sRNA for pollen development in Ogura-CMS Chinese Cabbage(Brassica rapa) Open
In this study, we focused on male sterility in Chinese cabbage, and selected anthers of both sterile (Tyms) and maintained (231-330) materials at the same period of time for specific study. The growth, and sampling conditions of sterile ma…
View article: Compressed sensing expands the multiplexity of imaging mass cytometry
Compressed sensing expands the multiplexity of imaging mass cytometry Open
The multiplexity of current antibody-based imaging is limited by the number of reporters that can be detected simultaneously. Compressed sensing can be used to reconstruct high-dimensional information from low-dimensional measurements. Pre…
View article: Paramylon isolated from Euglena gracilis EOD-1 extends lifespan through activation of DAF-16-mediated antioxidant pathway via clec-196 in Caenorhabditis elegans
Paramylon isolated from Euglena gracilis EOD-1 extends lifespan through activation of DAF-16-mediated antioxidant pathway via clec-196 in Caenorhabditis elegans Open
Paramylon (PM), an insoluble β-1,3-glucan produced by Euglena gracilis , reportedly possesses immunomodulatory and metabolic regulatory effects. However, its effect on longevity remains unclear. For this study, using Caenorhabditis elegans…
View article: Figure S1 from A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa
Figure S1 from A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa Open
Supplementary Figure S1. Measurement of RNA Quantity and Quality using PAXgene tissue container vs. RNAlater.
View article: Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth
Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth Open
Clb2 is a conserved B-type cyclin essential for mitotic progression in Saccharomyces cerevisiae , with expression tightly regulated at transcriptional and proteolytic levels. However, it remains unclear whether Clb2 protein synthesis is re…
View article: FMDV 3A cooperates with PDCD10 to promote FMDV replication by inhibiting VISA-mediated innate immunity
FMDV 3A cooperates with PDCD10 to promote FMDV replication by inhibiting VISA-mediated innate immunity Open
RIG-I like receptors (RLRs) recognize RNA viruses and induce an innate immune response. Although many host factors strictly regulate the signal transduction of the RLR pathway, the mechanisms remain unclear. In the present study, we demons…
View article: Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain
Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain Open
Pathological inclusions of the C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43) are neurodegenerative hallmarks in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, yet CTD’s aggregation propensity complicates …
View article: Alterations in Resident Immune Cells in Prenatal Trisomy 21 Lungs
Alterations in Resident Immune Cells in Prenatal Trisomy 21 Lungs Open
Respiratory tract infections (RTIs) are amongst the leading causes of hospitalizations in children with Down syndrome (DS). Their elevated susceptibility likely stems from structural differences in the airways and immune system abnormaliti…
View article: Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays
Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays Open
Introduction As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA seco…
View article: Identification of Novel TAT-I24-Related Peptides with Antiviral Activities
Identification of Novel TAT-I24-Related Peptides with Antiviral Activities Open
To identify novel peptides with potential antiviral activities, a database search was performed based on the primary sequence of the peptide I24 (CLAFYACFC), the effective part of the antiviral peptide TAT-I24 consisting of peptide I24 and…
View article: Methyladenine as a regulator of biomolecular condensation
Methyladenine as a regulator of biomolecular condensation Open
Ribonucleotide modifications modulate RNA structure and stability, thereby influencing RNA turnover and a wide range of cellular functions. Recent studies have revealed that specific RNA modifications can also affect the formation, composi…
View article: A programmable pAgo nuclease with high activity and specificity for efficient DNA and RNA manipulation
A programmable pAgo nuclease with high activity and specificity for efficient DNA and RNA manipulation Open
View article: Altered expression of LINC03091 and LINC03090 LncRNAs in bipolar disorder: a case-control study
Altered expression of LINC03091 and LINC03090 LncRNAs in bipolar disorder: a case-control study Open
Long non-coding RNAs (lncRNAs) are widely expressed and play an essential role in gene regulation through various transcriptional and post-transcriptional mechanisms. Recent findings have highlighted the role of lncRNAs in sustaining cellu…
View article: Resistance of first-line targeted drugs in hepatocellular carcinoma: the epigenetic regulation mechanisms
Resistance of first-line targeted drugs in hepatocellular carcinoma: the epigenetic regulation mechanisms Open
Targeted therapy has revolutionized the treatment landscape of hepatocellular carcinoma (HCC), offering unprecedented hope to patients. However, despite its promise, significant challenges arise in the form of drug resistance. Only a fract…
View article: Cardioprotective role of RBFox1 in myocardial infarction-induced heart failure
Cardioprotective role of RBFox1 in myocardial infarction-induced heart failure Open
Aims Alternative mRNA splicing is a significant part of transcriptome reprogramming during the pathological manifestation of heart diseases. Earlier studies have identified a muscle-specific isoform of RBFox1 (RNA binding fox-1 homolog 1) …
View article: Screening and Functional Analysis of tsRNAs Associated with Diabetic Foot Ulcer Tissues
Screening and Functional Analysis of tsRNAs Associated with Diabetic Foot Ulcer Tissues Open
Background: Diabetic foot ulcer (DFU) is a serious complication of diabetes mellitus, and its inability to heal is closely linked to vascular pathology. However, the specific molecular regulatory networks involved remain unclear. This stud…
View article: Global RNA-Interference Market: Trends, Applications, and Forecast (2023–2030)
Global RNA-Interference Market: Trends, Applications, and Forecast (2023–2030) Open
The global RNA-Interference (RNAi) Market was valued at USD 5.4 billion in 2023 and is projected to reach USD 14.7 billion by 2030, registering a CAGR of 15.3% from 2024 to 2030. RNAi technology selectively silences gene expression by targ…