scholarly journals RNA sequencing data for responses to drought stress and/or clubroot infection in developing seeds of Brassica napus

Data in Brief ◽  
2021 ◽  
pp. 107392
Author(s):  
Grégoire Bianchetti ◽  
Vanessa Clouet ◽  
Fabrice Legeai ◽  
Cécile Baron ◽  
Kévin Gazengel ◽  
...  
Keyword(s):  
Drought Stress ◽  
Brassica Napus ◽  
Rna Sequencing ◽  
Sequencing Data ◽  
Developing Seeds

scholarly journals Genome-Wide Survey and Expression Analysis of the KT/HAK/KUP Family in Brassica napus and Its Potential Roles in the Response to K+ Deficiency

2020 ◽  
Vol 21 (24) ◽  
pp. 9487
Author(s):  
Jie Zhou ◽  
Hong-Jun Zhou ◽  
Ping Chen ◽  
Lan-Lan Zhang ◽  
Jia-Tian Zhu ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Rna Sequencing ◽  
Expression Profiles ◽  
Small Scale ◽  
Sequencing Data ◽  
Element Analysis ◽  
Transporter Family ◽  
Group I ◽  
Large Expansion ◽  
K Deficiency

The KT/HAK/KUP (HAK) family is the largest potassium (K+) transporter family in plants, which plays key roles in K+ uptake and homeostasis, stress resistance, and root and embryo development. However, the HAK family has not yet been characterized in Brassica napus. In this study, 40 putative B. napus HAK genes (BnaHAKs) are identified and divided into four groups (Groups I–III and V) on the basis of phylogenetic analysis. Gene structure analysis revealed 10 conserved intron insertion sites across different groups. Collinearity analysis demonstrated that both allopolyploidization and small-scale duplication events contributed to the large expansion of BnaHAKs. Transcription factor (TF)-binding network construction, cis-element analysis, and microRNA prediction revealed that the expression of BnaHAKs is regulated by multiple factors. Analysis of RNA-sequencing data further revealed extensive expression profiles of the BnaHAKs in groups II, III, and V, with limited expression in group I. Compared with group I, most of the BnaHAKs in groups II, III, and V were more upregulated by hormone induction based on RNA-sequencing data. Reverse transcription-quantitative polymerase reaction analysis revealed that the expression of eight BnaHAKs of groups I and V was markedly upregulated under K+-deficiency treatment. Collectively, our results provide valuable information and key candidate genes for further functional studies of BnaHAKs.

A global survey of the transcriptome of allopolyploid Brassica napus based on single‐molecule long‐read isoform sequencing and Illumina‐based RNA sequencing data

2020 ◽  
Vol 103 (2) ◽  
pp. 843-857 ◽  
Author(s):  
Shengli Yao ◽  
Fan Liang ◽  
Rafaqat Ali Gill ◽  
Junyan Huang ◽  
Xiaohui Cheng ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Sequencing Data ◽  
Global Survey ◽  
Long Read

Investigation of the Dynamic Regulation Mechanisms of Small Non-Coding RNA in Response to Drought Stress in Qingke Barley

2019 ◽  
Author(s):  
Sang Zha ◽  
Thondup Gyalpo ◽  
Xingquan Zeng ◽  
Hongjun Yuan ◽  
Mingzhai Yu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Drought Resistance ◽  
Small Rna ◽  
Target Genes ◽  
Great Influence ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Characteristic Analysis ◽  
Non Coding Rna

Abstract Background Drought is a common abiotic stressor that exerts a great influence on grain security worldwide. The mechanisms underlying the small non-coding RNA regulation of plant drought responses remain unclear.Results In this study, drought-resistant (Xila-16, Xila) and drought-sensitive (DingqingHYG, Diqing) ecotypes were selected. A systematic analysis was performed on the microRNAs and tRNA-derived fragments in small RNA sequencing data. By predicting the target genes of differentially expressed miRNAs and analysing their pathway, this study identified HVUL2H01030.2, HVUL2H06276.2, HVUL2H00175.2 and other important target genes. The analysis also identified base excision repair and other adversity stress-related pathways. tRNA-derived fragments (tRFs), as a novel type of small noncoding RNA, exist widely in organisms, but no study has shown that tRFs play a role in the drought resistance of qingke barley. Based on systematic identification and characteristic analysis of tRFs in small RNA sequencing data, this study found that qingke barley had a tendency to produce more tRFs under drought stress. These tRFs were widely expressed, showed specific tRNA cleavage modes and had conservative intertreatment cleavage and other characteristics.Conclusions Our findings lay the foundation for further investigation of the action mechanism of such novel small noncoding RNAs in the drought resistance of qingke barley.

scholarly journals Transcriptome Analyses in Different Cucumber Cultivars Provide Novel Insights into Drought Stress Responses

2018 ◽  
Vol 19 (7) ◽  
pp. 2067 ◽  
Author(s):  
Min Wang ◽  
Biao Jiang ◽  
Qingwu Peng ◽  
Wenrui Liu ◽  
Xiaoming He ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Stress Responses ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Water Deficiency ◽  
Sequencing Data ◽  
Aba Signal Transduction ◽  
Drought Tolerant ◽  
Sucrose Biosynthesis

Drought stress is one of the most serious threats to cucumber quality and yield. To gain a good understanding of the molecular mechanism upon water deficiency, we compared and analyzed the RNA sequencing-based transcriptomic responses of two contrasting cucumber genotypes, L-9 (drought-tolerant) and A-16 (drought-sensitive). In our present study, combining the analysis of phenotype, twelve samples of cucumber were carried out a transcriptomic profile by RNA-Seq under normal and water-deficiency conditions, respectively. A total of 1008 transcripts were differentially expressed under normal conditions (466 up-regulated and 542 down-regulated) and 2265 transcripts under drought stress (979 up-regulated and 1286 down-regulated). The significant positive correlation between RNA sequencing data and a qRT-PCR analysis supported the results found. Differentially expressed genes (DEGs) involved in metabolic pathway and biosynthesis of secondary metabolism were significantly changed after drought stress. Several genes, which were related to sucrose biosynthesis (Csa3G784370 and Csa3G149890) and abscisic acid (ABA) signal transduction (Csa4M361820 and Csa6M382950), were specifically induced after 4 days of drought stress. DEGs between the two contrasting cultivars identified in our study provide a novel insight into isolating helpful candidate genes for drought tolerance in cucumber.

scholarly journals HEDGEHOG/GLI Modulates the PRR11-SKA2 Bidirectional Transcription Unit in Lung Squamous Cell Carcinomas

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 120
Author(s):  
Yiyun Sun ◽  
Dandan Xu ◽  
Chundong Zhang ◽  
Yitao Wang ◽  
Lian Zhang ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Squamous Cell ◽  
Gene Pair ◽  
Gene List ◽  
Ectopic Expression ◽  
Lung Squamous Cell Carcinoma ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Sequencing Data ◽  
Gene Set

We previously demonstrated that proline-rich protein 11 (PRR11) and spindle and kinetochore associated 2 (SKA2) constituted a head-to-head gene pair driven by a prototypical bidirectional promoter. This gene pair synergistically promoted the development of non-small cell lung cancer. However, the signaling pathways leading to the ectopic expression of this gene pair remains obscure. In the present study, we first analyzed the lung squamous cell carcinoma (LSCC) relevant RNA sequencing data from The Cancer Genome Atlas (TCGA) database using the correlation analysis of gene expression and gene set enrichment analysis (GSEA), which revealed that the PRR11-SKA2 correlated gene list highly resembled the Hedgehog (Hh) pathway activation-related gene set. Subsequently, GLI1/2 inhibitor GANT-61 or GLI1/2-siRNA inhibited the Hh pathway of LSCC cells, concomitantly decreasing the expression levels of PRR11 and SKA2. Furthermore, the mRNA expression profile of LSCC cells treated with GANT-61 was detected using RNA sequencing, displaying 397 differentially expressed genes (203 upregulated genes and 194 downregulated genes). Out of them, one gene set, including BIRC5, NCAPG, CCNB2, and BUB1, was involved in cell division and interacted with both PRR11 and SKA2. These genes were verified as the downregulated genes via RT-PCR and their high expression significantly correlated with the shorter overall survival of LSCC patients. Taken together, our results indicate that GLI1/2 mediates the expression of the PRR11-SKA2-centric gene set that serves as an unfavorable prognostic indicator for LSCC patients, potentializing new combinatorial diagnostic and therapeutic strategies in LSCC.

RNA Sequencing Data from Human Intracranial Aneurysm Tissue Reveals a Complex Inflammatory Environment Associated with Rupture

2021 ◽  
Author(s):  
Vincent M. Tutino ◽  
Haley R. Zebraski ◽  
Hamidreza Rajabzadeh-Oghaz ◽  
Lee Chaves ◽  
Adam A. Dmytriw ◽  
...  
Keyword(s):  
Intracranial Aneurysm ◽  
Rna Sequencing ◽  
Sequencing Data

scholarly journals In-depth transcriptomic analysis of human retina reveals molecular mechanisms underlying diabetic retinopathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kolja Becker ◽  
Holger Klein ◽  
Eric Simon ◽  
Coralie Viollet ◽  
Christian Haslinger ◽  
...  
Keyword(s):  
Diabetic Retinopathy ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Vision Loss ◽  
Ganglion Cells ◽  
Expression Profiles ◽  
Cell Types ◽  
Sequencing Data ◽  
Disease Stages ◽  
Post Transcriptional Regulation

AbstractDiabetic Retinopathy (DR) is among the major global causes for vision loss. With the rise in diabetes prevalence, an increase in DR incidence is expected. Current understanding of both the molecular etiology and pathways involved in the initiation and progression of DR is limited. Via RNA-Sequencing, we analyzed mRNA and miRNA expression profiles of 80 human post-mortem retinal samples from 43 patients diagnosed with various stages of DR. We found differentially expressed transcripts to be predominantly associated with late stage DR and pathways such as hippo and gap junction signaling. A multivariate regression model identified transcripts with progressive changes throughout disease stages, which in turn displayed significant overlap with sphingolipid and cGMP–PKG signaling. Combined analysis of miRNA and mRNA expression further uncovered disease-relevant miRNA/mRNA associations as potential mechanisms of post-transcriptional regulation. Finally, integrating human retinal single cell RNA-Sequencing data revealed a continuous loss of retinal ganglion cells, and Müller cell mediated changes in histidine and β-alanine signaling. While previously considered primarily a vascular disease, attention in DR has shifted to additional mechanisms and cell-types. Our findings offer an unprecedented and unbiased insight into molecular pathways and cell-specific changes in the development of DR, and provide potential avenues for future therapeutic intervention.

scholarly journals COVID-19 Severity Potentially Modulated by Cardiovascular-Disease-Associated Immune Dysregulation

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1018
Author(s):  
Abby C. Lee ◽  
Grant Castaneda ◽  
Wei Tse Li ◽  
Chengyu Chen ◽  
Neil Shende ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Expression Profiles ◽  
Immune Dysregulation ◽  
Left Ventricular ◽  
Recurrent Event ◽  
Healthy Controls ◽  
Sequencing Data ◽  
Peripheral Blood Mononuclear

Patients with underlying cardiovascular conditions are particularly vulnerable to severe COVID-19. In this project, we aimed to characterize similarities in dysregulated immune pathways between COVID-19 patients and patients with cardiomyopathy, venous thromboembolism (VTE), or coronary artery disease (CAD). We hypothesized that these similarly dysregulated pathways may be critical to how cardiovascular diseases (CVDs) exacerbate COVID-19. To evaluate immune dysregulation in different diseases, we used four separate datasets, including RNA-sequencing data from human left ventricular cardiac muscle samples of patients with dilated or ischemic cardiomyopathy and healthy controls; RNA-sequencing data of whole blood samples from patients with single or recurrent event VTE and healthy controls; RNA-sequencing data of human peripheral blood mononuclear cells (PBMCs) from patients with and without obstructive CAD; and RNA-sequencing data of platelets from COVID-19 subjects and healthy controls. We found similar immune dysregulation profiles between patients with CVDs and COVID-19 patients. Interestingly, cardiomyopathy patients display the most similar immune landscape to COVID-19 patients. Additionally, COVID-19 patients experience greater upregulation of cytokine- and inflammasome-related genes than patients with CVDs. In all, patients with CVDs have a significant overlap of cytokine- and inflammasome-related gene expression profiles with that of COVID-19 patients, possibly explaining their greater vulnerability to severe COVID-19.

scholarly journals IMMU-27. SINGLE CELL RNA-SEQUENCING IDENTIFIES NOVEL BONE MARROW DERIVED MYELOID CELLS IN GLIOBLASTOMA ASSOCIATED WITH TUMOR AGGRESSION

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii110-ii110
Author(s):  
Christina Jackson ◽  
Christopher Cherry ◽  
Sadhana Bom ◽  
Hao Zhang ◽  
John Choi ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Single Cell ◽  
Tumor Cells ◽  
Rna Sequencing ◽  
Metabolic Pathways ◽  
Myeloid Cells ◽  
Tumor Grade ◽  
Sequencing Data ◽  
Single Cell Rna Sequencing ◽  
Two Populations

Abstract BACKGROUND Glioma associated myeloid cells (GAMs) can be induced to adopt an immunosuppressive phenotype that can lead to inhibition of anti-tumor responses in glioblastoma (GBM). Understanding the composition and phenotypes of GAMs is essential to modulating the myeloid compartment as a therapeutic adjunct to improve anti-tumor immune response. METHODS We performed single-cell RNA-sequencing (sc-RNAseq) of 435,400 myeloid and tumor cells to identify transcriptomic and phenotypic differences in GAMs across glioma grades. We further correlated the heterogeneity of the GAM landscape with tumor cell transcriptomics to investigate interactions between GAMs and tumor cells. RESULTS sc-RNAseq revealed a diverse landscape of myeloid-lineage cells in gliomas with an increase in preponderance of bone marrow derived myeloid cells (BMDMs) with increasing tumor grade. We identified two populations of BMDMs unique to GBMs; Mac-1and Mac-2. Mac-1 demonstrates upregulation of immature myeloid gene signature and altered metabolic pathways. Mac-2 is characterized by expression of scavenger receptor MARCO. Pseudotime and RNA velocity analysis revealed the ability of Mac-1 to transition and differentiate to Mac-2 and other GAM subtypes. We further found that the presence of these two populations of BMDMs are associated with the presence of tumor cells with stem cell and mesenchymal features. Bulk RNA-sequencing data demonstrates that gene signatures of these populations are associated with worse survival in GBM. CONCLUSION We used sc-RNAseq to identify a novel population of immature BMDMs that is associated with higher glioma grades. This population exhibited altered metabolic pathways and stem-like potentials to differentiate into other GAM populations including GAMs with upregulation of immunosuppressive pathways. Our results elucidate unique interactions between BMDMs and GBM tumor cells that potentially drives GBM progression and the more aggressive mesenchymal subtype. Our discovery of these novel BMDMs have implications in new therapeutic targets in improving the efficacy of immune-based therapies in GBM.

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