rna-seq analysis of oil palm under cold stress reveals a ...

RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a ...

RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a Different C-Repeat Binding Factor (CBF) Mediated Gene Expression Pattern in Elaeis guineensis Compared to Other Species Xintao Lei , # 1 Yong Xiao , # 1, * Wei Xia , 1 Annaliese S. Mason , 3 Yaodong Yang , 1 Zilong Ma , 2 and Ming Peng 2

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rna-seq analysis of oil palm under cold stress reveals a ...

RNA-seq analysis of oil palm under cold stress reveals a ...

1. PLoS One. 2014 Dec 5;9(12):e114482. doi: 10.1371/journal.pone.0114482. eCollection 2014. RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.

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(pdf) rna-seq analysis of oil palm under cold stress reveals ...

(PDF) RNA-Seq Analysis of Oil Palm under Cold Stress Reveals ...

RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a Different C-Repeat Binding Factor (CBF) Mediated Gene Expression Pattern in Elaeis guineensis Compared to Other Species

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research article rna-seq analysis of oil palm under cold ...

RESEARCH ARTICLE RNA-Seq Analysis of Oil Palm under Cold ...

RESEARCH ARTICLE RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a Different C-Repeat Binding Factor (CBF) Mediated Gene Expression Pattern in Elaeis guineensis

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rna-seq analysis of oil palm under cold stress reveals a ...

RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a ...

Title: RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a Different C-Repeat Binding Factor (CBF) Mediated Gene Expression Pattern in Elaeis guineensis Compared to Other Species

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transcriptome analysis reveals key cold-stress-responsive ...

Transcriptome Analysis Reveals Key Cold-Stress-Responsive ...

Solexa/Illumina RNA sequencing (RNA-seq) has recently been used to identify cold tolerance genes in different species [12,13]. Studies investigating plant responses to cold stress have involved transcriptome profiling for many plant species [14], including Arabidopsis thaliana [12,15], Brassica

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rna-seq analysis reveals extensive transcriptional plasticity ...

RNA-seq analysis reveals extensive transcriptional plasticity ...

Over the past few years, the proliferation of software resources and validated pipelines for RNA-seq means that virtually any organism can now be the focus of ecological genomic research and this is reflected in the rapid increase in publications reporting RNA-seq analyses in non-human taxa.

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transcriptome analysis of oil palm inflorescences revealed ...

Transcriptome analysis of oil palm inflorescences revealed ...

Each oil palm inflorescence for each oil palm plant were produced in different times resulting a limitation in the amount inflorescences at the same pollination stage in the same plant. Consequently, we designed to compare RNA seq from the same stage but different oil palm plants as the treatments or controls at the given pollination stages.

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comparative transcriptome analysis of rna-seq data for cold ...

Comparative transcriptome analysis of RNA-seq data for cold ...

Abstract. Cold stress greatly affects plant growth and crop yield. To identify novel genes and possible mechanisms involved in chilling tolerance responses in rice seedlings, RNA sequencing (RNA-seq) technology was used for genome-wide gene expression profiling analysis to compare three cold-tolerant genotypes and one cold-sensitive genotype under both normal temperature and cold stress ...

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transcriptomics reveals multiple resistance mechanisms ...

Transcriptomics reveals multiple resistance mechanisms ...

Advances in the field of transcriptomics has made RNA-Sequencing (RNA-Seq) a major “-omics” technology for studying global gene expression of plants under different stress conditions 18,19 ...

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rna-seq analysis reveals extensive transcriptional plasticity ...

RNA-seq analysis reveals extensive transcriptional plasticity ...

Over the past few years, the proliferation of software resources and validated pipelines for RNA-seq means that virtually any organism can now be the focus of ecological genomic research and this is reflected in the rapid increase in publications reporting RNA-seq analyses in non-human taxa.

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transcriptome analysis reveals key cold-stress-responsive ...

Transcriptome Analysis Reveals Key Cold-Stress-Responsive ...

Solexa/Illumina RNA sequencing (RNA-seq) has recently been used to identify cold tolerance genes in different species [12,13]. Studies investigating plant responses to cold stress have involved transcriptome profiling for many plant species [14], including Arabidopsis thaliana [12,15], Brassica

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transcriptome analysis of flowering time genes under drought ...

Transcriptome Analysis of Flowering Time Genes under Drought ...

A change in flowering time is a strategy used to survive abiotic stresses. Among abiotic stresses, drought can increase anthesis-silking intervals (ASI), resulting in negative effects on maize yield. We have analyzed the correlation between flowering time and drought stress using RNA-seq and bioinformatics tools.

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transcriptome analysis of callus from melon - sciencedirect

Transcriptome analysis of callus from melon - ScienceDirect

Methods. The transcriptome sequencing analysis was used to analyze the mRNA sequence in embryogenic callus (Z) and non-embryogenic callus (F); transcript mapping, gene expression analysis, cluster analysis, classification analysis and enrichment analysis were then used to detect the differentially expressed genes and enriched pathways.

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rna-seq analysis, transcriptome assembly and gene expression ...

RNA-Seq analysis, transcriptome assembly and gene expression ...

RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for Zea may ssp. mexicana L. under cold and drought stress Purpose: The goals of this study are studies the response of annual Zea mays ssp. mexicana L. under cold and drought stress Methods: The seedlings of zea may ssp. mexicana L. were generated by Illumina ...

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rna‐seq reveals regional differences in transcriptome ...

RNA‐seq reveals regional differences in transcriptome ...

Snails from two southern (heat tolerant) and two northern (heat sensitive) populations were acclimated to a common thermal environment, exposed to an environmentally relevant thermal stress and analysed using RNA‐seq. Pooling across all populations revealed 306 genes with differential expression between control and heat‐stressed samples ...

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ming peng - academia.edu

Ming Peng - Academia.edu

RNA-Seq Analysis of Oil Palm under Cold Stress Reveals a Different C-Repeat Binding Factor (CBF) Mediated Gene Expression Pattern in Elaeis guineensis Compared to Other Species more

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single cardiomyocyte nuclear transcriptomes reveal a lincrna ...

Single cardiomyocyte nuclear transcriptomes reveal a lincRNA ...

Single nuclear RNA-seq reveals CM heterogeneity. a, b Core cardiac genes that are most highly expressed in every CM nucleus (a) exhibit high expression with low coefficient of variation (b).c ...

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rna-seq analysis in fruit science: a review :: science ...

RNA-Seq Analysis in Fruit Science: A Review :: Science ...

RNA-Seq analysis is an effective tool to understand which genes involved and expressed in different mechanisms and organs/cells of a plant. Recently, many articles have been published using RNA-Seq in fruits. In the present review, we illustrated how to apply different RNA-Seq platforms in fruits with examples.

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deep sequencing-based transcriptome profiling analysis in ...

Deep sequencing-based transcriptome profiling analysis in ...

such as the inherent cold-susceptibility of this energy plant. In this study, a powerful deep high-throughput sequencing approach, Illumina Hiseq™ 2000 RNA-seq (Wang et al., 2009), was exploited for transcriptome sequencing analysis of J. curcas from a mixed sampling of the untreated and cold-treated seedlings.

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deep sequencing-based transcriptome profiling analysis in ...

Deep sequencing-based transcriptome profiling analysis in ...

such as the inherent cold-susceptibility of this energy plant. In this study, a powerful deep high-throughput sequencing approach, Illumina Hiseq™ 2000 RNA-seq (Wang et al., 2009), was exploited for transcriptome sequencing analysis of J. curcas from a mixed sampling of the untreated and cold-treated seedlings.

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plos one: using rna-seq to profile gene expression of ...

PLOS ONE: Using RNA-seq to Profile Gene Expression of ...

Rice reproductive development is sensitive to high temperature and soil nitrogen supply, both of which are predicted to be increased threats to rice crop yield. Rice spikelet development is a critical process that determines yield, yet little is known about the transcriptional regulation of rice spikelet development in response to the combination of heat stress and low nitrogen availability.

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an rna-seq transcriptome analysis of orthophosphate-deficient ...

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient ...

The experiment was replicated three times (three biological replicates), resulting in a total of 12 cDNA libraries for RNA-Seq analysis. A total of 367,973,656 Illumina EST reads were generated from 12 cDNA libraries. After filtering homopolymers and short reads (less than 76 bp), a total of 277,224,180 reads (76 bp in size) were selected for ...

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frontiers | catalyzing plant science research with rna-seq ...

Frontiers | Catalyzing plant science research with RNA-seq ...

Bulked Segregant RNA-seq. Liu et al. (2012) demonstrated the application of RNA-seq for bulked segregant analysis (BSA) by mapping the maize mutant gene gl3.Transcriptome profiling is applied to a pool of two samples generated by mixing a bulk of mutant and wild-type (WT) plants (Figure 2).

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elymus nutans genes for seed shattering and candidate gene ...

Elymus nutans genes for seed shattering and candidate gene ...

Xiao et al. developed 182 gene-based SSR markers related to cold tolerance in oil palm by exploiting transcriptome data, and suggested these SSR markers would be particularly useful for gene mapping and population structure analysis in oil palm germplasm with different cold response.

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rna-seq reveals expression signatures of genes involved in ...

RNA-Seq reveals expression signatures of genes involved in ...

RNA-Seq analysis to identify heat stress-induced genes in catfish at the transcriptome level. Expression analysis identified a total of 2,260 differentially expressed genes with a cutoff of twofold change. qRT-PCR validation suggested the high reliability of the RNA-Seq results. Gene ontology, enrichment, and pathway analyses were conducted to

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transcriptome analysis of cucumber roots reveals key cold ...

Transcriptome Analysis of Cucumber Roots Reveals Key Cold ...

Cold stress is an important factor that limits the yield and quality of various agricultural plants worldwide. Symbiosis with arbuscular mycorrhizal fungi (AMF) could be an efficient way to help some plants resist cold stress. However, our understanding of the molecular mechanism concerning this particular process is limited.

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transcriptomic and phytochemical analysis of the biosynthesis ...

Transcriptomic and phytochemical analysis of the biosynthesis ...

Although oil tea (Camellia oleifera) belongs to the genus Camellia, this plant lacks these three characteristic constituents. Comparative analysis of tea and oil tea via RNA-Seq would help uncover the genetic components underlying the biosynthesis of characteristic metabolites in tea.

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mrna-seq analysis of the gossypiumarboreum transcriptome ...

mRNA-seq Analysis of the Gossypiumarboreum transcriptome ...

mRNA-seq Analysis of the Gossypiumarboreum transcriptome Reveals Tissue Selective Signaling in Response to Water Stress during Seedling Stage Xueyan Zhang1., Dongxia Yao2., Qianhua Wang1, Wenying Xu2, Qiang Wei2, Chunchao Wang2,

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single-cell map of diverse immune phenotypes in the breast ...

Single-Cell Map of Diverse Immune Phenotypes in the Breast ...

Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer.

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comparative transcriptome analysis reveals significant ...

Comparative transcriptome analysis reveals significant ...

The aim of this study, therefore, is to uncover the regulatory role of HCN in Arabidopsis and compare the significant differences in gene expression regulation with ET. RNA sequencing (RNA-seq) methods were used to analyse the differentially expressed genes (DEGs) after treatment with HCN and ET, compared to the control.

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integrated analysis of transcriptome and metabolites reveals ...

Integrated analysis of transcriptome and metabolites reveals ...

Currently, the molecular mechanism of a single stressor on starch accumulation in duckweed is yet to be revealed. In the current study, we performed a transcriptome survey to reveal the molecular mechanism of starch accumulation under nitrogen starvation in L. aequinoctialis 6000, which is a fast-growing and high starch species of duckweed.

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transcriptome analysis reveals anthocyanin acts as a ...

Transcriptome analysis reveals anthocyanin acts as a ...

They are found in various tissues and can protect plants against different stress... Transcriptome analysis reveals anthocyanin acts as a protectant in Begonia semperflorens under low temperature | SpringerLink

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dong chen | phd student | center for genome analysis

Dong Chen | PhD student | Center for Genome Analysis

ABLife, Inc. · Center for Genome Analysis. 18.33 · PhD ... with my RNA-seq differential expression analysis? ... and S. habrochaites leaf tissues under cold stress were studied using Illumina ...

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rna-seq analysis and targeted mutagenesis for improved free ...

RNA-Seq analysis and targeted mutagenesis for improved free ...

Results. Cyanobacterial FFA production was shown to generate reactive oxygen species (ROS) and lead to increased cell membrane permeability. To identify genetic targets that may mitigate these toxic effects, RNA-seq analysis was used to investigate the host response of Synechococcus elongatus PCC 7942.

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transcriptomic profiling of linolenic acid-responsive genes ...

Transcriptomic profiling of linolenic acid-responsive genes ...

Transcriptome analysis with the aid of RNA-seq in the absence of oxidative stress revealed that the incubation of Arabidopsis thaliana cell suspension cultures (ACSC) with Ln resulted in the modulation of 7525 genes, of which 3034 genes had a 2 fold-change, being 533 up- and 2501 down-regulated genes, respectively.

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frontiers | abiotic stresses modulate landscape of poplar ...

Frontiers | Abiotic Stresses Modulate Landscape of Poplar ...

Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms.

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multiple regression analysis reveals microrna regulatory ...

Multiple Regression Analysis Reveals MicroRNA Regulatory ...

Over the past decade, several drought-related miRNA families in rice have been identified by either microarray hybridization or RNA-seq [20, 21, 32]. Stress-responsive miRNAs regulate their target mRNAs by targeting the gene transcripts most of which are stress-associated functional proteins, e.g., transcription factors or hormones involved ...

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alternative splicing plays a major role in plant response to ...

Alternative Splicing Plays a Major Role in Plant Response to ...

Intriguingly, AS is likely important for regulating other stress response pathways in addition to cold tolerance. The advanced RNA-seq analysis system described by Calixto et al. could be used to explore AS in a variety of different contexts.

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loss of the rna polymerase iii repressor maf1 confers obesity ...

Loss of the RNA polymerase III repressor MAF1 confers obesity ...

eWAT RNA sequencing (RNA-seq) data were analyzed to determine the effect of the knockout on the synthesis of precursor tRNAs. These molecules are short-lived and are widely used to assess the level of transcription by RNA Pol III (Upadhya et al. 2002; Michels et al. 2010).

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transcriptome landscape of a bacterial pathogen under plant ...

Transcriptome landscape of a bacterial pathogen under plant ...

Despite extensive studies, how plant immunity ultimately inhibits bacterial pathogen growth is largely unknown, due to difficulties in profiling bacterial responses in planta . In this study, we established two methods for in planta bacterial transcriptome analysis using RNA sequencing.

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genome-wide identification and expression analysis of the hd ...

Genome-Wide Identification and Expression Analysis of the HD ...

stress. Finally, the expression profiles of the wheat HD-Zips in different tissues and under various abiotic stresses were investigated using the available RNA sequencing (RNA-Seq) data and then validated by quantitative real-time polymerase chain reaction (qRT-PCR) to obtain the tissue-specific and stress-responsive candidates.

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deep sequencing analysis of the methanosarcina mazei gö1 ...

Deep sequencing analysis of the Methanosarcina mazei Gö1 ...

Although all previous experimental approaches in archaea relied on cDNA cloning followed by Sanger sequencing, high-throughput sequencing of cDNA [RNA-seq ] has now revolutionized transcriptome analysis and sRNA discovery in many organisms (21–23). In the present work we used a recently developed differential RNA-seq method selective for ...

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gene expression profiles of brain endothelial cells during ...

Gene expression profiles of brain endothelial cells during ...

Although RNA sequencing (RNA-seq) permits profiling at high resolution, the relatively small number of ECs in the developing brain and the fact that these cells are dispersed among other cell types make it challenging to perform comprehensive profiling studies of the CNS endothelium.

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loss of the rna polymerase iii repressor maf1 confers obesity ...

Loss of the RNA polymerase III repressor MAF1 confers obesity ...

eWAT RNA sequencing (RNA-seq) data were analyzed to determine the effect of the knockout on the synthesis of precursor tRNAs. These molecules are short-lived and are widely used to assess the level of transcription by RNA Pol III (Upadhya et al. 2002; Michels et al. 2010).

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soybean dreb1/cbf‐type transcription factors function in heat ...

Soybean DREB1/CBF‐type transcription factors function in heat ...

Azzreena Mohamad Azzeme, Siti Nor Akmar Abdullah, Maheran Abd Aziz and Puteri Edaroyati Megat Wahab, Oil palm drought inducible DREB1 induced expression of DRE/CRT- and non-DRE/CRT-containing genes in lowland transgenic tomato under cold and PEG treatments, Plant Physiology and Biochemistry, 112, (129), (2017).

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medscape | mol genet genomics - publication information

Medscape | Mol Genet Genomics - Publication Information

Erratum to: Genome-wide analysis and expression patterns of ZF-HD transcription factors under different developmental tissues and abiotic stresses in Chinese cabbage. June 01, 2016 [ MEDLINE Abstract] Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping.

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understanding the biochemical basis of temperature-induced ...

Understanding the Biochemical Basis of Temperature-Induced ...

RNA Sequencing and Data Analysis. Total RNA was extracted from eight samples (four biological replicates for each growth condition) of A. lentiformis leaf tissues grown at 23°C and 43°C using the Agilent Plant RNA isolation kit (Agilent Technologies). Eight cDNA libraries were constructed from leaves with four biological replicates for each ...

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rna-seq analysis and targeted mutagenesis for improved free ...

RNA-Seq analysis and targeted mutagenesis for improved free ...

Results. Cyanobacterial FFA production was shown to generate reactive oxygen species (ROS) and lead to increased cell membrane permeability. To identify genetic targets that may mitigate these toxic effects, RNA-seq analysis was used to investigate the host response of Synechococcus elongatus PCC 7942.

Get Price
a single-cell survey of the human first-trimester placenta ...

A single-cell survey of the human first-trimester placenta ...

Here, we report single-cell RNA sequencing of 14,341 and 6754 cells from first-trimester human placental villous and decidual tissues, respectively. Bioinformatic analysis identified major cell types, many known and some subtypes previously unknown in placental villi and decidual context.

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