Overexpression of a B3 Transcription Factor CsFUS3 Promotes Somatic Embryogenesis of citrus through the Abscisic Acid and Gibberellin
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ABSTRACT:
ORGANISM(S): Citrus unshiu
PROVIDER: GSE69193 | GEO | 2016/05/23
SECONDARY ACCESSION(S): PRJNA284785
REPOSITORIES: GEO
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Project description:To determine the transcriptional response to Salmonella enterica serovar Enteritidis (SE) infection, a newly developed chicken 44K Agilent array was used to analyze total RNA of heterophils from SE-resistant (line A) and SE–susceptible chickens (line B), treated with in vitro infection of SE (I) or non SE medium (N) for 1 hr. A dual-color balanced design was used to provide a direct comparison between SE-infected and non-infected groups (AI/AN, BI/BN) and between line A and line B (AN/BN, AI/BI). Data retrieved from 426 immunologically important genes were used for functional analysis. The results indicated that: In the comparisons of SE infection with non-infection, 39 genes were found differentially expressed (P < 0.05 with at least 2-fold) after Salmonella infection, while 21 genes were found differentially expressed between different lineages. Numerous of members in Toll-like receptor (TLR) signaling pathway were identified which include receptors: MD-2, TLR-4, -5, -15; adaptors: TLR adaptor molecule1 (TICAM1/TRIF), MAP kinase kinase 3 (MKK3) and NFkB-1, as well as cytokines, chemokines and costimulatory molecule: interleukin (IL)-1β, IL-6, IL-8, IL-12, chemokine (C-X-C motif) ligand 1, chemokine (C-C motif) ligand 4, CCL 5, and CD80. Most of immune genes were up-regulated after SE infection, and the magnitude of up-regulation was higher in line A than line B in general. The results suggested that a similar TLR regulatory network exists in both lines with strong response in resistant line. This finding has laid the foundation for further study of molecular and cellular modulation of SE infection in chickens. Keywords: disease state analysis
2008-09-01 | GSE9416 | GEO
Project description:Purpose: In this study we investigated the role of JASMONATE RESISTANT 1 (JAR1) and JAR1 mediated JA-Ile formation in drought stress tolerance in Arabidopsis thaliana. Methods: Global transcriptional changes in a newly generated over-expression line (JAR1-OE; 35S::JAR1-1-YFP)), a T-DNA insertion line in the JAR1 locus (jar1-11;SALK_034543), and wild-type Col-0 were investigated by RNA-seq analyses of rosette leaves from 32 day-old plant that were either well-watered (control) or not watered after day 18 (drought). Plants were grown on soil under long-day conditions Results: Under control conditions, using a stringent cut-off (DESeq, adjusted to FDR < 0.01 and LogFC ≥ 1), we found only four differentially expressed genes (DEGs) between jar1-11 and Col-0, all of them downregulated. By contrast, we found 339 DEGs between JAR1-OE and Col-0, of which 134 were downregulated and 205 were upregulated. A comparison of the RNA-seq data from Col-0 between control and drought conditions revealed 3401 DEGs, of which 2023 were down- and 1378 upregulated. By comparison, jar1-11 plants, which were most heavily affected by drought stress, showed a much higher number (6139 in total; 2616 up- and 3523 down-regulated) of DEGs, while the more drought-tolerant JAR1-OE line displayed a lower number (2025 in total; 971 up- and 1054 down-regulated) of DEGs. 2411 DEGs were found between Col-0 and jar1-11 under drought among which 966 genes showed a higher and 1445 genes a lower expression level in jar1-11. On the other hand, out of 998 DEGs found between Col-0 and JAR1-OE under drought, 737 genes showed a higher and 261 genes a lower expression level in JAR1-OE. Moreover, we found 391 DEGs counter-regulated between jar1-11 and JAR1-OE. Conclusion:RNA-seq analysis and additional experiments of plants under control and drought stress conditions provided insight into the molecular reprogramming caused by the alteration in JA-Ile content.
2022-07-25 | GSE196602 | GEO
Project description:Mitogen-activated protein kinases usually affect biological processes by phosphorylating proteins. To further investigate the consequences of MAPK11 interacting with SnRK1 in controlling tomato seed dormancy, we performed a phosphorylation label-free quantitative proteomic assay in vivo with dry seeds of TS-9and MAPK11-OE lines. Data analysis showed that a total of 8261 phosphosites and 6026 phosphopeptides derived from 2711 phosphoproteins were identified. The phosphopeptides with an average fold-change >2 or <0.5 and a P value <0.05 were selected as being significantly different. Among all identified phosphopeptides, 87 phosphopeptides were significantly up-regulated and 83 phosphopeptides were significantly down-regulated in seeds of MAPK11-OE line. In addition, we also found that 348 phosphopeptides were just abundant in MAPK11-OE-13 line, and 221 phosphopeptides merely in TS-9, respectively. To explore potential biological function of MAPK11, we conducted GO function annotation and enrichment, KEGG passway annotation and enrichment, and protein protein interaction network (PPI) analyses, and detected that MAPK11 might have effect on binding, catalytic activity, transporter activity, molecular function regulator and signal transducer; and involved in cellular process, metabolic process, biological regulation, regulation of biological process and response to stimulus
2020-12-02 | PXD013026 | Pride
Project description:To determine the transcriptional response to Salmonella enterica serovar Enteritidis (SE) infection, a newly developed chicken 44K Agilent array was used to analyze total RNA of heterophils from SE-resistant (line A) and SEâsusceptible chickens (line B), treated with in vitro infection of SE (I) or non SE medium (N) for 1 hr. A dual-color balanced design was used to provide a direct comparison between SE-infected and non-infected groups (AI/AN, BI/BN) and between line A and line B (AN/BN, AI/BI). Data retrieved from 426 immunologically important genes were used for functional analysis. The results indicated that: In the comparisons of SE infection with non-infection, 39 genes were found differentially expressed (P < 0.05 with at least 2-fold) after Salmonella infection, while 21 genes were found differentially expressed between different lineages. Numerous of members in Toll-like receptor (TLR) signaling pathway were identified which include receptors: MD-2, TLR-4, -5, -15; adaptors: TLR adaptor molecule1 (TICAM1/TRIF), MAP kinase kinase 3 (MKK3) and NFkB-1, as well as cytokines, chemokines and costimulatory molecule: interleukin (IL)-1β, IL-6, IL-8, IL-12, chemokine (C-X-C motif) ligand 1, chemokine (C-C motif) ligand 4, CCL 5, and CD80. Most of immune genes were up-regulated after SE infection, and the magnitude of up-regulation was higher in line A than line B in general. The results suggested that a similar TLR regulatory network exists in both lines with strong response in resistant line. This finding has laid the foundation for further study of molecular and cellular modulation of SE infection in chickens. Keywords: disease state analysis A dual color, balanced design was carried on for all of heterophils samples from sixteen chickens. Each sample type (AI, AN, BI and BN) includes four biological replication for labeling. A Dye swap was used in each pair of comparisons including AI/AN, BI/BN, and AI/BI, and AN/BN. Background subtracted signal intensity were collected from 16 arrays and normalized for data analysis.
2010-06-20 | E-GEOD-9416 | biostudies-arrayexpress
Project description:Purpose: Comparing the transcriptome of wild-type(N2), hlh-11 knock-out and hlh-11 over-expression worms to identify genes with differential expression. Methods: For each condition, two replicates were examined. For each sample, approximately 2,000 synchronized young adult worms were collected and resuspended in TRIzon Reagent (CW0580, CWBIO). Total RNA was isolated by chloroform extraction, followed by isopropanol precipitation. Sequencing was performed using HiSeq2500. The clean reads were aligned to WBcel235 genomes with TopHat2. Gene differential expression was analyzed using DEseq2. A threshold of p < 0.05 was set to determine differentially expressed genes. Induction (KO_up or OE_up) or suppression (KO_down or OE_down) of genes were obtained through comparing gene expressions in hlh-11 KO or OE worms to wild-type N2. Results: >86% reads were uniquely mapped. 2637 genes were significantly up regulated and 2845 genes were significantly down regulated in hlh-11 knock-out worms compared to wild-type. 107 genes were significantly up regulated and 237 genes were significantly down regulated in hlh-11 over-expression worms compared to wild-type. Conclusions: This study revealed the genes transcriptionally regulated by hlh-11.
2019-11-23 | GSE140866 | GEO
Project description:To investigate the function of NAC094 in vivo, we overexpressed NAC094 in the infected cells of nodules using an L. japonicus Lb2 expression cassette. To this end, we used a GUS overexpression construct as control and analysed stably transformed plants to detect symbiotic phenotypes. Results show that overexpression of NAC094 causes premature senescence of nodules. To identify the mechanism by which NAC094 regulates nodule senescence, we performed a transcriptome profiling analysis of nodules at 3 wpi. Around 13,850 differentially expressed genes (DEGs) were identified by comparing NAC-OE with control nodules (Log2FC > 1, FDR < 0.05). Of these, 7,516 were up-regulated (NAC-OE-UP) and 6,334 were down-regulated (NAC-OE-DOWN).
2023-03-23 | GSE197361 | GEO
Project description:The goals of this study are to find the target gene of ARF18, to explain why the ARF18 overexpression line has smaller leaves. Library construction and sequencing were performed as described elsewhere, based on RNA extracted with the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) from 7-day-old seedlings of 35S-ARF18-OE-2 and Col. The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5’ and 3’ RNA adaptor-ligated using T4 RNA ligase and amplified for 18 PCR cycles. The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China). Raw reads were trimmed by removing low-quality and adaptor sequences, and then they were aligned to the Arabidopsis genome using SOAP2 software. Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the p value and the false discovery rate (FDR) (Audic and Claverie, 1997). The chosen thresholds were FDR ≤ 0.001 and |log2| ≥ 1. We identified 113 differentially expressed genes, of which 49 genes are up-regulated, and 94 genes are down-regulated.
2018-10-16 | GSE121222 | GEO
Project description:Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy in need of new therapeutic options. Using an unbiased analysis of super-enhancers (SEs) as sentinels of core genes involved in cell-specific function, we uncover a druggable SE-mediated RNA-binding protein (RBP) cascade that supports PDAC growth through enhanced mRNA translation. This cascade is driven by a SE associated with the RBP heterogeneous nuclear ribonucleoprotein F, which stabilizes protein arginine methyltransferase 1 (PRMT1) to, in turn, control the translational mediator ubiquitin-associated protein 2-like. All three of these genes and the regulatory SE are essential for PDAC growth and coordinately regulated by the Myc oncogene. In line with this, modulation of the RBP network by PRMT1 inhibition reveals a unique vulnerability in Myc-high PDAC patient organoids and markedly reduces tumor growth in vivo. Our study highlights a functional link between epigenetic regulation and mRNA translation and identifies components that comprise unexpected therapeutic targets for PDAC.
2023-06-15 | PXD030423 | Pride
Project description:Purpose: The goals of this study are to investigate the effect of PKM2 KO or TMEM33 overexpression on genes expression. Methods: Fresh PKM2 KO MCF7, PKM2 KO MDA-MB-231 and TMEM33 OE MDA-MB-231 cell pellets, and their respective parental cells, were used for RNA extraction. RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer’s instructions. Each library was sequenced in single read mode, 1 x 50 bp, using the HiSeq4000 platform. Sequencing reads were aligned to human genome (hg38) by STAR (version 2.5.2b). Expression levels of genes annotated in GENCODE (version 24 for PKM2 KO and their parental cells; version 27 for TMEM33 OE and their control cells) were quantified by RSEM (version 1.3.0). Parameters of STAR and RSEM were set following ENCODE’s long RNA-seq processing pipeline. Differentially expressed genes were identified by DESeq2 (version 1.24.0) under the requirement of at least two-fold changes and an adjusted p-value < 0.05. Results: Differential gene expression analyses identified 269 and 504 significantly up-regulated and 204 and 289 significantly down-regulated genes in MDA-MB-231 and MCF7 PKM2 KO cells compared to their parental cells (>=2-fold, adjusted P value < 0.05); Gene set enrichment analysis (GSEA) showed that cholesterol homeostasis and fatty acid metabolism were among the top down-regulated pathways in MDA-MB-231 TMEM33 OE cells. Moreover, the differential gene expression profiles between PKM2 KO and TMEM33 OE cell lines were positively correlated. Notably, the mRNAs of genes related to cholesterol homeostasis were decreased in both PKM2 KO and TMEM33 OE cells. Conclusions: TMEM33 acts as a downstream effector of PKM2 that regulates activation of SREBPs and lipid metabolism.
2021-08-06 | GSE175956 | GEO
Project description:Conditional Bmp4 overexpression (Bmp4 OE), using a tetracycline regulated Bmp4 gain of function allele, resulted in facial skeletal changes that were most dramatic after an E10.5 Bmp4 induction. We identified a number of genes predominantly transcriptional regulators controlling self-renewal, osteoblast differentiation, and negative Bmp autoregulation whose expression were change after Bmp4 overexpression in the cranial neural crest cells. We performed expression profiling using RNA extracted from E11.5 Bmp4 OE mandibles that were induced with dox for 24 hours. Using a 2-fold change (p< 0.05) as threshold, we identified 144 down-regulated and 120 up-regulated genes.
2011-12-17 | E-GEOD-34502 | biostudies-arrayexpress