Profiling bacterial transcriptome is challenging due to the low abundance of bacterial RNA in infected plant tissues. Here, we describe a protocol to profile transcriptome of a foliar bacterial pathogen, pv. DC3000, in the leaves of at an early stage of infection using RNA sequencing (RNA-Seq). Bacterial cells are first physically isolated from infected leaves, followed by RNA extraction, plant rRNA depletion, cDNA library synthesis, and RNA-Seq. This protocol is likely applicable not only to the pathosystem but also to different plant-bacterial combinations.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8328654 | PMC |
| http://dx.doi.org/10.21769/BioProtoc.2987 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Background: TAR-DNA-binding protein 43 (TDP43), is a pathologic marker in neurodegenerative diseases including frontotemporal lobar degeneration and amyotrophic lateral sclerosis. The aggregation of TDP-43, a crucial RNA-binding protein, is a consequence of post-translational modifications (PTMs) that disrupt its normal function. PTMs such as phosphorylation and ubiquitination contribute to the aberrant accumulation of TDP-43 aggregates, leading to neurodegenerative disorders like amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD).
View Article and Find Full Text PDFIntegrated Network Pharmacology and Transcriptomics Analysis to Elucidate the Mechanism of Huoxue Tongluo Qiwei Decoction in the Treatment of Erectile Dysfunction in Spontaneously Hypertensive Rats through Angii-Activated Pkcε Pathway.
Comb Chem High Throughput Screen
January 2025
Department of Andrology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China.
Background And Aim: As a classical formula to invigorate blood circulation, Huoxue Tongluo Qiwei Decoction (HTQD) can effectively treat hypertensive erectile dysfunction (ED), but its exact mechanism of action is not yet clear. The goal of this research was to explore the potential mechanism of HTQD in improving hypertensive erectile dysfunction in rats through transcriptomics, network pharmacology, and associated animal experimentations.
Methods: The HTQD chemical constituents were screened using high-performance liquid chromatography- tandem mass spectrometry (HPLC-MS/MS).
Establishment of a Prognostic Necroptosis-Related lncRNA Signature in Ovarian Cancer.
Comb Chem High Throughput Screen
January 2025
Department of Gynecology, Affiliated Xingtai People Hospital of Hebei Medical University, China.
Introduction: Ovarian Cancer (OC) was known for its high mortality rate among gynecological malignancies, often resulting in a poor prognosis. This study sought to identify prognostic necroptosis-related long non-coding RNAs (lncRNAs) (NRlncRNAs) with prognostic potential and to construct a reliable risk prediction model for OC patients.
Method: The transcriptome and clinic data were sourced from TCGA and GTEx databases.
Exploring vimentin's role in breast cancer via PICK1 alternative polyadenylation and the miR-615-3p-PICK1 interaction.
Biofactors
January 2025
Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Tongji University, Shanghai, People's Republic of China.
Breast cancer continues to be a major health issue for women worldwide, with vimentin (VIM) identified as a crucial factor in its progression due to its role in cell migration and the epithelial-to-mesenchymal transition (EMT). This study focuses on elucidating VIM's regulatory mechanisms on the miR-615-3p/PICK1 axis. Utilizing the 4T1 breast cancer cell model, we first used RNA-seq and proteomics to investigate the changes in the APA of PICK1 following VIM knockout (KO).
View Article and Find Full Text PDFSpecifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs.
NAR Genom Bioinform
March 2025
Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden.
Understanding the role of transcription and transcription factors (TFs) in cellular identity and disease, such as cancer, is essential. However, comprehensive data resources for cell line-specific TF-to-target gene annotations are currently limited. To address this, we employed a straightforward method to define regulons that capture the cell-specific aspects of TF binding and transcript expression levels.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!