RNA-sequencing Analysis of Differentially Expressed Genes in Wild-type andBnERF-transgenic Arabidopsis Under Submergence Treatment

2015 ◽  
Vol 50 (3) ◽  
pp. 321
Author(s):  
Lü Yanyan ◽  
Fu Sanxiong ◽  
Chen Song ◽  
Zhang Wei ◽  
Qi Cunkou
Keyword(s):  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Transgenic Arabidopsis ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Wild Type

Identification of Differentially Expressed and Spliced Genes with RNA Sequencing Analysis of CLL Specimens

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4582-4582
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Artur Jaroszewicz ◽  
Matteo Pellegrini ◽  
Sanjai Sharma
Keyword(s):  
B Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Fold Change ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Core Set

Abstract Abstract 4582 High throughput sequencing of cellular mRNA provides a comprehensive analysis of the transcriptome. Besides identifying differentially expressed genes in different cell types, it also provides information of mRNA isoforms and splicing alterations. We have analyzed two CLL specimens and a normal peripheral blood B cells mRNA by this approach and performed data analysis to identify differentially expressed and spliced genes. The result showed CLLs specimens express approximately 40% more transcripts compared to normal B cells. The FPKM data (fragment per kilobase of exon per million) revealed a higher transcript expression on chromosome 12 in CLL#1 indicating the presence of trisomy 12, which was confirmed by fluorescent in-situ hybridization assay. With a two-fold change in FPKM as a cutoff and a p value cutoff of 0.05 as compared to the normal B cell control, 415 genes and 174 genes in CLL#1 and 676 and 235 genes in CLL#2 were up and downregulated or differentially expressed. In these two CLL specimens, 45% to 75% of differentially expressed genes are common to both the CLL specimens indicating that genetically disparate CLL specimens have a high percentage of a core set of genes that are potentially important for CLL biology. Selected differentially expressed genes with increased expression (selectin P ligand, SELPLG, and adhesion molecule interacts with CXADR antigen 1, AMICA) and decreased (Fos, Jun, CD69 and Rhob) expression based on the FPKM from RNA-sequencing data were also analyzed in additional CLL specimens by real time PCR analysis. The expression data from RNA-seq closely matches the fold-change in expression as measured by RT-PCR analysis and confirms the validity of the RNA-seq analysis. Interestingly, Fos was identified as one of the most downregulated gene in CLL. Using the Cufflinks and Cuffdiff software, the splicing patterns of genes in CLL specimens and normal B cells were analyzed. Approximately, 1100 to 1250 genes in the two CLL specimens were significantly differentially spliced as compared to normal B cells. In this analysis as well, there is a core set of 800 common genes which are differentially spliced in the two CLL specimens. The RNA-sequencing analysis accurately identifies differentially expressed novel genes and splicing variations that will help us understand the biology of CLL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv + MDV in chickens

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kunzhe Dong ◽  
Shuang Chang ◽  
Qingmei Xie ◽  
Peng Zhao ◽  
Huanmin Zhang
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Host Defense ◽  
Tumor Suppression ◽  
Genetic Resistance ◽  
Early Mortality ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Latent Phase

Abstract Very virulent plus Marek’s disease (MD) virus (vv + MDV) induces tumors in relatively resistant lines of chickens and early mortality in highly susceptible lines of chickens. The vv + MDV also triggers a series of cellular responses in both types of chickens. We challenged birds sampled from a highly inbred chicken line (line 63) that is relatively resistant to MD and from another inbred line (line 72) that is highly susceptible to MD with a vv + MDV. RNA-sequencing analysis was performed with samples extracted from spleen tissues taken at 10-day and 21-day post infection (dpi). A total of 64 and 106 differentially expressed genes was identified in response to the vv + MDV challenge at latent phase in the resistant and susceptible lines of chickens, respectively. Direct comparisons between samples of the two lines identified 90 and 126 differentially expressed genes for control and MDV challenged groups, respectively. The differentially expressed gene profiles illustrated that intensive defense responses were significantly induced by vv + MDV at 10 dpi and 21 dpi but with slight changes in the resistant line. In contrast, vv + MDV induced a measurable suppression of gene expression associated with host defense at 10 dpi but followed by an apparent activation of the defense response at 21 dpi in the susceptible line of chickens. The observed difference in gene expression between the two genetic lines of chickens in response to MDV challenge during the latent phase provided a piece of indirect evidence that time points for MDV reactivation differ between the genetic lines of chickens with different levels of genetic resistance to MD. Early MDV reactivation might be necessary and potent to host defense system readiness for damage control of tumorigenesis and disease progression, which consequently results in measurable differences in phenotypic characteristics including early mortality (8 to 20 dpi) and tumor incidence between the resistant and susceptible lines of chickens. Combining differential gene expression patterns with reported GO function terms and quantitative trait loci, a total of 27 top genes was selected as highly promising candidate genes for genetic resistance to MD. These genes are functionally involved with virus process (F13A1 and HSP90AB1), immunity (ABCB1LB, RGS5, C10ORF58, OSF-2, MMP7, CXCL12, GAL1, GAL2, GAL7, HVCN1, PDE4D, IL4I1, PARP9, EOMES, MPEG1, PDK4, CCLI10, K60 and FST), and tumor suppression (ADAMTS2, LXN, ARRDC3, WNT7A, CLDN1 and HPGD). It is anticipated that these findings will facilitate advancement in the fundamental understanding on mechanisms of genetic resistance to MD. In addition, such advancement may also provide insights on tumor virus-induced tumorigenesis in general and help the research community recognize MD study may serve as a good model for oncology study involving tumor viruses.

scholarly journals PSII-11 RNA sequencing analysis reveals differentially expressed genes and novel upstream transcriptional regulators in porcine longissimus dorsi muscle affected by dietary lysine restriction

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 233-233
Author(s):  
Ying Wang ◽  
Huaijun Zhou ◽  
Shengfa F Liao
Keyword(s):  
Protein Synthesis ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Muscle Protein ◽  
Transcriptional Regulators ◽  
Growing Pigs ◽  
Differentially Expressed ◽  
Longissimus Dorsi ◽  
Sequencing Analysis ◽  
Rna Seq

Abstract The objective of this research was to investigate the effects of dietary lysine restriction on the global gene expression of skeletal muscle in growing pigs. Twelve crossbred (Yorkshire × Landrace) barrows (initial BW 22.6 ± 2.04 kg) were randomly assigned to two dietary treatments (Diet I: a lysine-deficient diet; Diet II: a lysine-adequate diet) according to a completely randomized experiment design (n = 6). After feeding for 8 weeks, muscle samples were collected from longissimus dorsi of individual pigs (approximately 2 g/each). The total RNA isolated was used to prepare cDNA library for RNA sequencing (RNA-Seq) analysis. The RNA-Seq data was then analyzed using the CLC Genomics Workbench to identify differentially expressed genes (DEGs). Sixty-nine genes were found differentially expressed (Benjamin-Hochberg corrected P < 0.05) in Diet I vs. Diet II pigs, of which 29 genes were down-regulated (Log₂ fold change (FC) < - 0.58) and 40 genes were up-regulated (Log₂ FC > 0.58). Gene ontology (GO) analysis of these DEGs for functional annotation using DAVID found a total of 36 GO terms. The significantly enriched terms (Benjamin-Hochberg corrected P < 0.05) are associated with biological processes that include acute-phase response, platelet activation, and protein polymerization, and Molecular Functions that include serine-type endopeptidase inhibitor activity, small molecule binding, heme binding, and oxidoreductase activity. In addition, Ingenuity Pathway Analysis predicted some upstream transcriptional regulators that regulate several sets of DEGs. For example, lysine restriction may lead inhibition of insulin, EIF2AK4 (an eIF2α activator), and MYC (a transcript elongation factor), which are associated with the regulation of protein synthesis. It may also lead activation of STAT3 and HNF1A, which regulate cell movement and fatty acid metabolism, respectively. In summary, these novel results showed that dietary lysine restriction may compromise pig muscle protein synthesis through the aforementioned transcriptional regulators and their affected genes.

scholarly journals RNA Sequencing Analysis of Molecular Basis of Sodium Butyrate-Induced Growth Inhibition on Colorectal Cancer Cell Lines

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Qianwen Zhou ◽  
Guiqin Li ◽  
Siyu Zuo ◽  
Wenjing Zhu ◽  
Xiaoqin Yuan
Keyword(s):  
Colorectal Cancer ◽  
Cell Death ◽  
Cancer Cells ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Sodium Butyrate ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Inhibition Of Proliferation ◽  
Colorectal Cancer Cells

Butyrate is a short-chain fatty acid decomposed from dietary fiber and has been shown to have effects on inhibition of proliferation but induction of apoptosis in colorectal cancer cells. However, clinical trials have yielded ambiguous outcomes with regard to its antitumor activities. In this study, we aimed to explore the molecular mechanisms underlying the sensitivity of colorectal cancer cells to sodium butyrate (NaB). RNA sequencing was used to establish the whole-transcriptome profile in NaB-treated versus untreated colorectal cancer cells. Differentially expressed genes were bioinformatically analyzed to predict their possible involvement in NaB-triggered cell death, and the expression of eight dysregulated genes was validated by quantitative real-time PCR. We found that there were a total of 7192 genes (5720 upregulated and 1472 downregulated, fold-change ≥ 2 or ≤ 0.5 for upregulation or downregulation, q-value < 0.05) differentially expressed in NaB-treated cells as compared with the untreated controls. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated that the differentially expressed genes were enriched in DNA replication, cell cycle, homologous recombination, pyrimidine metabolism, mismatch repair, and other signaling pathways and may take part in NaB-induced cell death. Among the identified factors, the MCM2-7 complex might be a target of NaB. Our findings provide an important basis for further studies of the complicate network that might regulate sensitivity of colorectal cancer cells to NaB.

RNA sequencing analysis reveals differential gene expression of CXCL2 in ACPA-positive and ACPA-negative rheumatoid arthritis

2020 ◽  
Author(s):  
Lin Sun ◽  
Xinyu Wang ◽  
Ning He ◽  
Zhuo An ◽  
Ruohan Yu ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Enzyme Linked Immunosorbent Assay ◽  
Sequencing Analysis ◽  
Healthy Controls ◽  
Raw264.7 Macrophages

Abstract Background. Anti-citrullinated protein/peptide antibodies (ACPA) play important roles in the pathogenesis of rheumatoid arthritis (RA), and are associated with RA severity. It has been suggested that ACPA-positive (ACPA+) and ACPA-negative (ACPA-) RA are different disease subsets with distinct differences in genetic variation and clinical outcomes. The aims of the present study were to compare gene expression profiles in ACPA + and ACPA- RA and identify novel candidate gene signatures that might serve as therapeutic targets. Methods. Comprehensive transcriptome analysis of peripheral blood mononuclear cells (PBMCs) from ACPA + and ACPA- RA patients, and healthy controls was performed via RNA sequencing. Genes with significantly different expressions were analyzed by cluster analysis, Gene Ontology analysis and Ingenuity Pathway analysis. A validation cohort was used to further investigate differentially expressed genes via real-time PCR and enzyme-linked immunosorbent assay. Spearman's correlation test was used to evaluate the correlation of differentially expressed genes and the clinical and laboratory data of the patients. The role of differentially expressed genes in osteoclastogenesis was further investigated. Results. There were significant differences in the expression levels of both genes and gene isoforms between ACPA + and ACPA- RA samples. Expression of C-X-C motif chemokine ligand 2 (CXCL2) was significantly increased in ACPA + RA patients than in ACPA- RA patients and healthy controls. Validation of candidate genes expression showed that CXCL2 levels in PBMCs and serum were higher in ACPA + RA patients than in ACPA- RA patients and healthy controls. CXCL2 promoted the migration of CD14 + monocytes and increased osteoclast differentiation in RA patients. RAW264.7 macrophages were used to investigate specific mechanisms, and the results suggested that CXCL2 stimulated osteoclastogenesis via ERK MAPK and NFκB pathways. Conclusion. Novel pathways associated with ACPA + RA were identified via RNA sequencing, and CXCL2 was highly expressed in ACPA + RA than in ACPA- RA. These results reveal a previously unreported role of CXCL2 during osteoclastogenesis in RA, and suggest that the blockade of CXCL2 might be a novel strategy for the treatment of RA.

scholarly journals Identification of Differentially Expressed Genes in Mice with Nutritional or Genetic Causes of Iron Overload

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2681-2681
Author(s):  
Aaron Cheng ◽  
Luke Schissler ◽  
Bonnie Patchen ◽  
Vera Gaun ◽  
Manoj Bhasin ◽  
...  
Keyword(s):  
Iron Overload ◽  
Differentially Expressed Genes ◽  
Knockout Mice ◽  
Bone Morphogenic Protein ◽  
Genetic Models ◽  
Differentially Expressed ◽  
Sequencing Analysis ◽  
Dietary Iron ◽  
Wild Type ◽  
Iron Deficient

Abstract Iron overload causes the generation of reactive oxygen species, which can lead to lasting organ damage, particularly to the liver. In patients with hereditary hemochromatosis, transfusion-dependent anemias, and hemoglobinopathies, iron overload is a major cause of mortality. A deeper understanding of iron regulation and the biological pathways involved in maintaining homeostasis may reveal new therapeutic targets for patients with iron overload disorders. We designed this study to discover genes that are differentially expressed in nutritional and genetic models of iron overload. For the nutritional iron overload study, 5-week old male C57BL/6 mice were placed on a soy-free diet (AIN-93G) containing different amounts of iron per kilogram of food: iron-deficient (2.5 mg/kg, n=3), iron-sufficient (37.5 mg/kg, n=3), and iron-excess (750 mg/kg, n=3). In the second study, 5-week old male C57BL/6 mice that were either wild type or HJV knockout mice that exhibited severe early onset iron overload secondary to homozygous deficiency of the bone morphogenic protein coreceptor, hemojuvelin (HJV), were maintained on the iron-deficient (2.5 mg/kg iron) diet (n=2 per group). For both studies animals were sacrificed after 50 days and liver RNA was extracted and sequenced at 40-50 million reads per sample. The RNA integrity number (RIN) for each sample was >6 and assessments of read duplication, base call frequency, and read quality indicated excellent quality of the data. For the HJV knockout mice, we used a false discovery rate <0.05 and a mean-fold change >2, to reveal genes that were differentially expressed compared to wild type mice. For the dietary iron study, genes were grouped by self-organizing maps to identify transcripts whose level of expression trended with increased or decreased dietary iron intake. The resulting analysis identified 148 genes in nutritionally iron-overloaded mice and 688 genes in HJV knockout mice that exhibited significant changes in expression. Of these, 28 genes were differentially regulated in both nutritionally iron overloaded and HJV knockout mice, including expected genes, such as transferrin receptor, HAMP (hepcidin), and bone morphogenic protein 6, and unexpected genes such as cytochrome P450 17a1 (cyp17a1), an enzyme that catalyzes critical steps in steroid synthesis, and nicotinomide N-methyltransferase (nnmt), an enzyme that regulates drug metabolism and DNA methylation. We clustered the 688 differentially expressed genes from the HJV knockout mice into functional pathways using the Functional Analysis tool from DAVID Bioinformatics Resources 6.7 (NIAID). Clusters were considered significant if there were >2 genes in the pathway and the Benjamini-Hochberg P-value was <0.05. We found that the expression of genes involved with PPAR signaling (P=0.0086) was decreased, while expression of transcripts involved with Huntington’s disease (P=0.038) was increased in HJV knockout mice compared to wild-type mice. Our RNA sequencing analysis identified a variety of novel pathways that were differentially regulated in dietary and genetic models of iron overload. Further studies are underway to characterize the potential roles of these genes in iron homeostasis. Disclosures No relevant conflicts of interest to declare.

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