16,709 results match your criteria rna-seq data

Identifying genomic regions targeted during eggplant domestication using transcriptome data.

J Hered 2021 Jun 15. Epub 2021 Jun 15.

Biological Sciences, University of Southampton, Southampton, UK.

Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A 'bottom up' population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data was obtained for four wild eggplants (Solanum insanum L. Read More

View Article and Full-Text PDF

Altered canalicular remodeling associated with femur fracture in mice.

J Orthop Res 2021 Jun 15. Epub 2021 Jun 15.

University of California Davis Health, Department of Orthopaedic Surgery.

We previously showed that femur fracture in mice caused a reduction in bone volume at distant skeletal sites within 2 weeks post-fracture. Osteocytes also have the ability to remodel their surrounding bone matrix through perilacunar/canalicular remodeling (PLR). If PLR is altered systemically following fracture, this could affect bone mechanical properties and increase fracture risk at all skeletal sites. Read More

View Article and Full-Text PDF

Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.

Oncogene 2021 Jun 14. Epub 2021 Jun 14.

Institute of Biomedicine, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland.

Treatment of prostate cancer confronts resistance to androgen receptor (AR)-targeted therapies. AR-associated coregulators and chromatin proteins hold a great potential for novel therapy targets. Here, we employed a powerful chromatin-directed proteomics approach termed ChIP-SICAP to uncover the composition of chromatin protein network, the chromatome, around endogenous AR in castration resistant prostate cancer (CRPC) cells. Read More

View Article and Full-Text PDF

Genome-wide detection and analysis of CRISPR-Cas off-targets.

Prog Mol Biol Transl Sci 2021 4;181:31-43. Epub 2021 Mar 4.

Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States; Department of Molecular, Cell and Cancer Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States. Electronic address:

The clustered, regularly interspersed, short palindromic repeats (CRISPR) technology is revolutionizing biological studies and holds tremendous promise for treating human diseases. However, a significant limitation of this technology is that modifications can occur on off-target sites lacking perfect complementarity to the single guide RNA (sgRNA) or canonical protospacer-adjacent motif (PAM) sequence. Several in vivo and in vitro genome-wide off-target profiling approaches have been developed to inform on the fidelity of gene editing. Read More

View Article and Full-Text PDF

Genome-Wide Essentiality Analysis of by Saturated Transposon Mutagenesis and Deep Sequencing.

mBio 2021 Jun 15:e0104921. Epub 2021 Jun 15.

The Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.

Mycobacterium abscessus is an emerging opportunistic human pathogen that naturally resists most major classes of antibiotics, making infections difficult to treat. Thus far, little is known about physiology, pathogenesis, and drug resistance. Genome-wide analyses have comprehensively catalogued genes with essential functions in Mycobacterium tuberculosis and Mycobacterium avium subsp. Read More

View Article and Full-Text PDF

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.

Nucleic Acids Res 2021 Jun 14. Epub 2021 Jun 14.

Center for Computational and Molecular Biology, Brown University, Providence, RI 02912, USA.

Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Read More

View Article and Full-Text PDF

Cell type hierarchy reconstruction via reconciliation of multi-resolution cluster tree.

Nucleic Acids Res 2021 Jun 14. Epub 2021 Jun 14.

Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.

A wealth of clustering algorithms are available for single-cell RNA sequencing (scRNA-seq) data to enable the identification of functionally distinct subpopulations that each possess a different pattern of gene expression activity. Implementation of these methods requires a choice of resolution parameter to determine the number of clusters, and critical judgment from the researchers is required to determine the desired resolution. This supervised process takes significant time and effort. Read More

View Article and Full-Text PDF

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq.

J Vis Exp 2021 May 28(171). Epub 2021 May 28.

Department of Developmental and Cell Biology, University of California, Irvine;

Distilling and reporting large datasets, such as whole genome or transcriptome data, is often a daunting task. One way to break down results is to focus on one or more gene families that are significant to the organism and study. In this protocol, we outline bioinformatic steps to generate a phylogeny and to quantify the expression of genes of interest. Read More

View Article and Full-Text PDF

N--Feruloyloctopamine Wakes Up BBC3, DDIT3, CDKN1A, and NOXA Signals to Accelerate HCC Cell Apoptosis.

Anal Cell Pathol (Amst) 2021 22;2021:1560307. Epub 2021 May 22.

General Surgery Department, The First Hospital of Lanzhou University, The First Clinical Medical College, Lanzhou University, Lanzhou 730000, Gansu Province, China.

N--Feruloyloctopamine (FO), a natural compound, was reported in our previous study to inhibit a tumor cell malignant phenotype by AKT- and EMT-related signals and might be used as a promising drug for HCC treatment. However, the specific targets and detailed mechanisms still need to be clarified. Screening with RNA-Seq in Huh7 cells treated with FO revealed that 317 genes were modulated, of which 188 genes were upregulated and 129 genes were downregulated. Read More

View Article and Full-Text PDF

Logical modelling of differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions.

Interface Focus 2021 Jun 11;11(4):20200061. Epub 2021 Jun 11.

Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, México.

Dendritic cells (DCs) are the major specialized antigen-presenting cells, thereby connecting innate and adaptive immunity. Because of their role in establishing adaptive immunity, they constitute promising targets for immunotherapy. Monocytes can differentiate into DCs in the presence of colony-stimulating factor 2 (CSF2) and interleukin 4 (IL4), activating four signalling pathways (MAPK, JAK/STAT, NFKB and PI3K). Read More

View Article and Full-Text PDF

AutoEncoder-Based Computational Framework for Tumor Microenvironment Decomposition and Biomarker Identification in Metastatic Melanoma.

Front Genet 2021 27;12:665065. Epub 2021 May 27.

Department of Medicine, Baylor College of Medicine, Houston, TX, United States.

Melanoma is one of the most aggressive cancer types whose prognosis is determined by both the tumor cell-intrinsic and -extrinsic features as well as their interactions. In this study, we performed systematic and unbiased analysis using The Cancer Genome Atlas (TCGA) melanoma RNA-seq data and identified two gene signatures that captured the intrinsic and extrinsic features, respectively. Specifically, we selected genes that best reflected the expression signals from tumor cells and immune infiltrate cells. Read More

View Article and Full-Text PDF

REW-ISA V2: A Biclustering Method Fusing Homologous Information for Analyzing and Mining Epi-Transcriptome Data.

Front Genet 2021 28;12:654820. Epub 2021 May 28.

Engineering Research Center of Intelligent Control for Underground Space, China University of Mining and Technology, Ministry of Education, Xuzhou, China.

Previous studies have shown that N6-methyladenosine (mA) is related to many life processes and physiological and pathological phenomena. However, the specific regulatory mechanism of mA sites at the systematic level is not clear. Therefore, mining the RNA co-methylation patterns in the epi-transcriptome data is expected to explain the specific regulation mechanism of mA. Read More

View Article and Full-Text PDF

PSDX: A Comprehensive Multi-Omics Association Database of With a Focus on the Secondary Growth in Response to Stresses.

Front Plant Sci 2021 20;12:655565. Epub 2021 May 20.

Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.

() is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in . However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Read More

View Article and Full-Text PDF

Identification and Analysis of bZIP Family Genes in Potato and Their Potential Roles in Stress Responses.

Front Plant Sci 2021 28;12:637343. Epub 2021 May 28.

Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China.

The bZIP proteins comprise one of the largest transcription factor families and play important roles in plant growth and development, senescence, metabolic reactions, and stress responses. In this study, 49 bZIP transcription factor-encoding genes ( genes) on the potato genome were identified and analyzed. The 49 genes, which are located on 12 chromosomes of the potato genome, were divided into 11 subgroups together with their homologs based on the results of phylogenetic analysis. Read More

View Article and Full-Text PDF

Transcriptomic Analysis of Ovine Hepatic Lymph Node Following Infection - Inhibition of NK Cell and IgE-Mediated Signaling.

Front Immunol 2021 28;12:687579. Epub 2021 May 28.

UCD School of Veterinary Medicine, Dublin, Ireland.

is a trematode parasite responsible for major economic losses in livestock production, and is also a food-borne zoonotic agent in developing rural regions. For years, the immunoregulatory mechanisms employed by the parasite have hampered efforts to develop a successful vaccine candidate. Given that a comprehensive understanding of the immune response to infection is needed, we investigated the gene expression changes in ovine hepatic lymph nodes after experimental infection with . Read More

View Article and Full-Text PDF

Integrated Analysis of Omics Data Reveal AP-1 as a Potential Regulation Hub in the Inflammation-Induced Hyperalgesia Rat Model.

Front Immunol 2021 28;12:672498. Epub 2021 May 28.

Department of Anesthesiology, Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, China.

Inflammation-associated chronic pain is a global clinical problem, affecting millions of people worldwide. However, the underlying mechanisms that mediate inflammation-associated chronic pain remain unclear. A rat model of cutaneous inflammation induced by Complete Freund's Adjuvant (CFA) has been widely used as an inflammation-induced pain hypersensitivity model. Read More

View Article and Full-Text PDF

Comprehensive Comparison of RNA-Seq Data of SARS-CoV-2, SARS-CoV and MERS-CoV Infections: Alternative Entry Routes and Innate Immune Responses.

Front Immunol 2021 28;12:656433. Epub 2021 May 28.

Bioinformatics and Computational Biophysics, Faculty of Biology and Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.

Background: The pathogenesis of COVID-19 emerges as complex, with multiple factors leading to injury of different organs. Some of the studies on aspects of SARS-CoV-2 cell entry and innate immunity have produced seemingly contradictory claims. In this situation, a comprehensive comparative analysis of a large number of related datasets from several studies could bring more clarity, which is imperative for therapy development. Read More

View Article and Full-Text PDF

Transcriptome-Wide N-Methyladenosine (mA) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific mA Modification Involved in Virus-Host Interaction Pathways.

Front Microbiol 2021 26;12:656302. Epub 2021 May 26.

State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China.

N-methyladenosine (mA) methylation is the most prevalent internal modification of post-transcriptional modifications in mRNA, tRNA, miRNA, and long non-coding RNA in eukaryotes. mA methylation has been proven to be involved in plant resistance to pathogens. However, there are no reports on wheat () mA transcriptome-wide map and its potential biological function in wheat resistance to wheat yellow mosaic virus (WYMV). Read More

View Article and Full-Text PDF

Attenuated Induction of the Unfolded Protein Response in Adult Human Primary Astrocytes in Response to Recurrent Low Glucose.

Front Endocrinol (Lausanne) 2021 26;12:671724. Epub 2021 May 26.

Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Exeter, United Kingdom.

Aims/hypothesis: Recurrent hypoglycaemia (RH) is a major side-effect of intensive insulin therapy for people with diabetes. Changes in hypoglycaemia sensing by the brain contribute to the development of impaired counterregulatory responses to and awareness of hypoglycaemia. Little is known about the intrinsic changes in human astrocytes in response to acute and recurrent low glucose (RLG) exposure. Read More

View Article and Full-Text PDF

Expression of Urea Transporter B in Normal and Injured Brain.

Front Neuroanat 2021 28;15:591726. Epub 2021 May 28.

Department of Anatomy, Laboratory of Neuroscience and Tissue Engineering, Basic Medical College, Chongqing Medical University, Chongqing, China.

Urea transporter B (UT-B) is a membrane channel protein widely distributed in mammals, and plays a significant physiological role by regulating urea and water transportation in different tissues. More and more studies have found that UT-B is related to neurological diseases, including myelinopathy and depression. When urea accumulates in the brains of UT-B knockout mice, the synaptic plasticity of neurons is reduced, and the morphology and function of glial cells are also changed. Read More

View Article and Full-Text PDF

Single-cell immune checkpoint landscape of PBMCs stimulated with .

Emerg Microbes Infect 2021 Jun 14:1-38. Epub 2021 Jun 14.

Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, China.

Immune checkpoints play various important roles in tumor immunity, which usually contribute to T cells' exhaustion, leading to immunosuppression in the tumor microenvironment. However, the roles of immune checkpoints in infectious diseases, especially fungal infection, remain elusive. Here, we reanalyzed a recent published single-cell RNA-sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) stimulated with (), to explore the expression patterns of immune checkpoints after bloodstream infection. Read More

View Article and Full-Text PDF

G-protein-coupled receptor GPR17 inhibits glioma development by increasing polycomb repressive complex 1-mediated ROS production.

Cell Death Dis 2021 Jun 12;12(6):610. Epub 2021 Jun 12.

State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, China.

Glioma is the most common primary tumor in the central nervous system. However, the development of glioma and effective therapeutic strategies remain elusive. Here, we identify GPR17 as a potential target to treat glioma. Read More

View Article and Full-Text PDF

Comparative transcriptome analysis reveals a potential mechanism for host nutritional manipulation after parasitization by Leptopilina boulardi.

Comp Biochem Physiol Part D Genomics Proteomics 2021 Jun 7;39:100862. Epub 2021 Jun 7.

Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China. Electronic address:

Parasitoids have been extensively found to manipulate nutrient amounts of their hosts to benefit their own development and survival, but the underlying mechanisms are largely unknown. Leptopilina boulardi (Hymenoptera: Figitidae) is a larval-pupal endoparasitoid wasp of Drosophila melanogaster whose survival relies on the nutrients provided by its Drosophila host. Here, we used RNA-seq to compare the gene expression levels of the host midgut at 24 h and 48 h post L. Read More

View Article and Full-Text PDF

Full-length transcriptome sequence analysis of Eimeria necatrix unsporulated oocysts and sporozoites identifies genes involved in cellular invasion.

Vet Parasitol 2021 Jun 2;296:109480. Epub 2021 Jun 2.

College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China. Electronic address:

Eimeria necatrix is one of the most pathogenic chicken coccidia and causes avian coccidiosis, an enteric disease of major economic importance worldwide. Eimeria parasites have complex developmental life cycles, with an exogenous phase in the environment and an endogenous phase in the chicken intestine. Oocysts excreted by chickens rapidly undergo meiosis and cell division to form eight haploid sporozoites (SZ). Read More

View Article and Full-Text PDF

lncRNA BSG-AS1 is hypoxia-responsive and promotes hepatocellular carcinoma by enhancing BSG mRNA stability.

Biochem Biophys Res Commun 2021 Jun 10;566:101-107. Epub 2021 Jun 10.

The Department of Pathology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, China. Electronic address:

Emerging evidence indicates that aberrant changes of lncRNAs expression induced by hypoxia participate in the development of HCC. The present study aimed to identify novel hypoxia-responsive lncRNAs and reveal its role and mechanism in HCC. Hypoxia exposure in HCC tissues was comprehensively estimated based on public data using multiple hypoxia gene signatures. Read More

View Article and Full-Text PDF

Overexpression of human BAG3 in mice causes restrictive cardiomyopathy.

Nat Commun 2021 06 11;12(1):3575. Epub 2021 Jun 11.

Institute of Physiology I, Life and Brain Center, Medical Faculty, University of Bonn, Bonn, Germany.

An amino acid exchange (P209L) in the HSPB8 binding site of the human co-chaperone BAG3 gives rise to severe childhood cardiomyopathy. To phenocopy the disease in mice and gain insight into its mechanisms, we generated humanized transgenic mouse models. Expression of human BAG3-eGFP in mice caused Z-disc disintegration and formation of protein aggregates. Read More

View Article and Full-Text PDF

Integrative Analysis of Genome, 3D Genome, and Transcriptome Alterations of Clinical Lung Cancer Samples.

Genomics Proteomics Bioinformatics 2021 Jun 8. Epub 2021 Jun 8.

Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China. Electronic address:

Genomic studies of cancer cell alterations, such as mutations, copy number variations (CNVs), and translocations, greatly promote our understanding of the genesis and development of cancer. However, the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical difficulties. To explore the 3D genome structure in clinical lung cancer, we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer, combining with RNA-seq analysis. Read More

View Article and Full-Text PDF

SC1: A Tool for Interactive Web-Based Single-Cell RNA-Seq Data Analysis.

J Comput Biol 2021 Jun 11. Epub 2021 Jun 11.

Computer Science and Engineering Department, University of Connecticut, Storrs, Connecticut, USA.

Single-cell RNA-Seq (scRNA-Seq) is critical for studying cellular function and phenotypic heterogeneity as well as the development of tissues and tumors. In this study, we present a web-based highly interactive scRNA-Seq data analysis tool publicly accessible at https://sc1.engr. Read More

View Article and Full-Text PDF

A novel ferroptosis-related gene signature for prognostic prediction of patients with lung adenocarcinoma.

Aging (Albany NY) 2021 Jun 11;13. Epub 2021 Jun 11.

Department of Microbiology and Immunology, Institute of Molecular Virology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China.

Background: Lung adenocarcinoma (LUAD) is a heterogeneous disease characterized by high mortality and poor prognosis. Ferroptosis, a newly discovered iron-dependent type of cell death, has been found to play a crucial role in the development of cancers. However, little is known about the prognostic value of ferroptosis-related genes (FRGs) in LUAD. Read More

View Article and Full-Text PDF

Analysis of expression characteristics of soybean leaf and root tissue-specific promoters in Arabidopsis and soybean.

Transgenic Res 2021 Jun 11. Epub 2021 Jun 11.

Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, 130033, Changchun, China.

The characterization of tissue-specific promoters is critical for studying the functions of genes in a given tissue/organ. To study tissue-specific promoters in soybean, we screened tissue-specific expressed genes using published soybean RNA-Seq-based transcriptome data coupled with RT-PCR analysis. We cloned the promoters of three genes, GmADR1, GmBTP1, and GmGER1, and constructed their corresponding β-Glucuronidase (GUS) promoter-GUS reporter vectors. Read More

View Article and Full-Text PDF