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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

ABSTRACT: We focused on RNA-seq-based full transcriptome responses to PtrSND1-B1 overexpression at 7, 12, and 25 h in stem defferentiating xylem (SDX) protoplasts We transfected PtrSND1-B1 and sGFP into stem differentiating xylem protoplasts and performed RNA-seq to reveal the whole transcriptome.

ORGANISM(S): Populus trichocarpa

SUBMITTER: Ying-Chung Lin

PROVIDER: E-GEOD-49911 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa.

Lin Ying-Chung YC Li Wei W Sun Ying-Hsuan YH Kumari Sapna S Wei Hairong H Li Quanzi Q Tunlaya-Anukit Sermsawat S Sederoff Ronald R RR Chiang Vincent L VL

The Plant cell 20131126 11

Wood is an essential renewable raw material for industrial products and energy. However, knowledge of the genetic regulation of wood formation is limited. We developed a genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)-directed hierarchical gene regulatory networks (hGRNs) in wood formation. This system depends on a new robust procedure for isolation and transfection of Populus trichocarpa stem differentiating xylem protoplasts. We overexp ...[more]

PMID: 24280390

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SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa

Project description:We focused on RNA-seq-based full transcriptome responses to PtrSND1-B1 overexpression at 7, 12, and 25 h in stem defferentiating xylem (SDX) protoplasts

2014-04-01 | GSE49911 | GEO

Transcriptome of Protoplasts Reprogrammed into Stem Cells in Physcomitrella patens

Project description:We obtained genome-wide digital gene expression tag profiles within the first three days of P. patens protoplast reprogramming. At four time-points during protoplast reprogramming, the transcript levels of 4827 genes changed more than four-fold and their expression correlated with the reprogramming phase. Gene ontology (GO) and pathway enrichment analysis of differentially expressed genes (DEGs) identified a set of significantly enriched GO terms and pathways, most of which were associated with photosynthesis, protein synthesis and stress responses. DEGs were grouped into six clusters that showed specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes identified a number of key candidate genes and pathways in early stages of protoplast reprogramming, which provided important clues to reveal the molecular mechanisms responsible for protoplast reprogramming. We identified genes that show highly dynamic changes in expression during protoplast reprogramming into stem cells in P. patens. These genes are potential targets for further functional characterization and should be valuable for exploration of the mechanisms of stem cell reprogramming. In particular, our data provides evidence that protoplasts of P. patens are an ideal model system for elucidation of the molecular mechanisms underlying differentiated plant cell reprogramming. Examination of 4 different sampling times.

2015-02-28 | E-GEOD-36117 | biostudies-arrayexpress

RNA-seq of five Populus x canescens (Grey poplar) organs/tissues during periodic or chronic drought-heat stress treatment and after recovery in comparison to untreated controls

Project description:Simulating predicted future climate conditions, stress response and stress-related memory after one week of recovery were transcriptionally characterised in young and old leaves, phloem-bark, developing xylem and roots of 3-month-old Grey poplar plants that had undergone three weeks of stress or were kept under control conditions. The control conditions include ambient or elevated CO2 levels (380 μL L-1 and 500 μL L-1, respectively) with a daily maximum temperature of 27 °C. The stress conditions include a periodic and a chronic drought-heat scenario at elevated CO2 levels (500 μL L-1) with a daily maximum temperature of 33 °C. The periodic stress treatment included three cycles of reduced irrigation (50%, 60% and 70% reduction compared with the controls), each one lasting for six days; between the cycles, there were recovery periods with a duration of two days and a daily maximum temperature of 27 °C. In the chronic stress treatment, irrigation was gradually reduced for 22 days, down to 70% reduction compared with the controls. Three biological replicates were examined per group defined by a specific environmental condition (droughtPER: periodic stress, droughtCHR: chronic stress, control500: elevated CO2 control, control380: ambient CO2 control), a specific harvesting time (S: stress phase, R: recovery phase) and a specific tissue (LE1: young leaves, LE2: old leaves, PHL: phloem-bark, XYL: developing xylem, ROO: roots). For stress phase ambient CO2 control in old leaves, one replicate failed quality control.

2019-01-11 | E-MTAB-6121 | biostudies-arrayexpress

Transcription profiling of Populus x canescens developing and mature xylem under short-days and drought stress treatment

Project description:Populus x canescens were kept in climate chambers for a growing period of 8 weeks. Afterwards, treatment started for five weeks in total. Plant were first treated with different daylength (long-days or short-days) under well-watered conditions. After 2 weeks, half of each daylength treatment was drought stressed while the other half was still well-watered. After further three weeks, all poplars were harvested and samples of developing and mature xylem were taken and directly frozen in liquid nitrogen. These samples were taken for RNA extraction and following RNA-sequencing.

2018-10-21 | E-MTAB-7288 | biostudies-arrayexpress

Identification of wild soybean miRNAs and their target genes responsive to aluminum stress

Project description:In this study, two small RNA libraries and two degradome libraries were constructed from roots of Al-treated and Al-free Glycine soja seedlings. For miRNA, a total of 7,287,655 and 7,035,914 clean reads in Al-treated and Al-free small RNAs libraries were generated, and 105 known miRNAs ,51 p3/p5 strands of known miRNA and 80 novel miRNAs were identified. Among them, expression of 34 miRNAs was responsive to Al stress. Through degradome sequencing, 82 and 11 genes were identified as tagerts of known and novel miRNAs obtained from this study, respectively. Gene Ontology (GO) annotations of target transcripts indicated that 52 out of 66 targets cleaved by conserved miRNA families may play role in regulation of transcription. sample 1: Examination of small RNA in Al-free wild soybean roots; sampple 2: Examination of small RNA in Al-treated wild soybena roots; sample 3: identification of miRNA targets in Al-free wild soybean roots; sample 4: identification of miRNA targerts in Al-treated wild soybean roots

2012-05-25 | E-GEOD-38065 | biostudies-arrayexpress

Methylation Changes During Soybean Seed Development

Project description:What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation during the transition from seed differentiation to maturation and dormany in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB stage), maturation (early- (EM), mid- (B1) and late- (AA1) maturation stages), and dormancy (DRY stage) phases of soybean seed development using Illumina sequencing. In addition, we characterized the methylome of the mid-maturation stage embryonic axis (B1-AX) to examine methylation differences, if any, between an embryonic region compared to the whole seed. Illumina sequencing of bisulfite-converted genomic DNA from globular stage (GLOB), early-maturation stage (EM), mid-maturation stage (B1), and late-maturation stage (AA1) seeds, dormancy stage (DRY) and mid-maturation embryonic axis (B1-AX).

2011-12-22 | E-GEOD-34637 | biostudies-arrayexpress

Transcriptome analysis of poplar during leaf spot infection with Sphaerulina spp.

Project description:Diseases of poplar caused by the fungal pathogen Sphaerulina musiva and related species are of growing concern, particular with the increasing interest in intensive popluliculture to meet increasing energy demands. S. musiva is able to cause infection on leaves, resulting in defoliation and canker formation on stems. To gain a greater understanding of the different responses of poplar species to infection with their natural Sphaerulina species, RNA-seq was conducted on leaves of Populus deltoides, P. balsamifera and P. tremuloides infected with S. musiva, S. populicola and a new undescribed species Ston1, respectively. Progression of disease symptoms, pathogen growth and host response were detected. Through the time course of infection, different and species-specific metabolic pathways were activated. In all three species, genes associated with growth and development were down-regulated, while genes involved the phenylpropanoid, terpenoid and flavonoid biosynthesis were up-regulated. Poplar defensive genes were expressed early in P. balsamifera and P. tremuloides, but delayed in P. deltoides, which correlated with the rate of disease symptoms development. This data gives an insight into the large differences in timing and expression of genes between poplar species being attacked with their native associated Sphaerulina pathogen. RNA-seq was conducted on leaves of Populus deltoides, P. balsamifera and P. tremuloides infected with S. musiva, S. populicola and a new undescribed species Ston1, respectively.

2015-08-28 | E-GEOD-67697 | biostudies-arrayexpress

Methylation Changes in Soybean Mid-Maturation Seed Parts

Project description:Seeds are comprised of three majors parts of distinct parental origin: the seed coat, embryo, and endosperm. The maternally-derived seed coat is important for nurturing and protecting the seeds during development. By contrast, the embryo and the endosperm are derived from a double fertilization event, where one sperm fertilizes the egg to form the diploid zygote and the other sperm fertilizes the central cell to form the triploid endosperm. Each seed parts undergo distinct developmental programs during seed development. What methylation changes occurring in the different seed parts, if any, remains unknown. To uncover the possible role of DNA methylation in different parts of the seed, we characterized the methylome of three major parts of an early maturation stage seed: seed coat, embryonic cotyledons, and embryonic axis using Illumina sequencing. Illumina sequencing of bisulfite-converted genomic DNA from three parts of an mid-maturation (B1) stage seed: seed coat (B1-SC), embryonic cotyledons (B1-COT), and embryonic axis (B1-AX).

2013-08-26 | E-GEOD-41061 | biostudies-arrayexpress

RNA-Seq Profiling of a Defective Seed Coat Mutation in Glycine max Reveals Differential Expression of Proline Rich and Other Cell Wall Protein Transcripts

Project description:The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. The genome-wide comparative study of the transcript profiles of these isolines revealed 364 differentially expressed genes in common between the two varieties that were further divided into different broad functional categories. Genes related to cell wall processes accounted for 19% of the differentially expressed genes in the middle developmental stage of 100-200 mg seed weight. Within this class, the cell wall proline-rich and glycine-rich protein genes were highly differentially expressed in both genetic backgrounds. Other genes that showed significant expression changes in each of the isoline pairs at the 100-200 mg seed weight stage were xylem serine proteinase, fasciclin-related genes, auxin and stress response related genes, TRANSPARENT TESTA 1 (TT1) and other transcription factors. The mutant appears to shift the timing of either the increase or decrease in the levels of some of the transcripts. The analysis of these data sets reveals the physiological changes that the seed coat undergoes during the formation of the breaks in the cell wall. Examination of soybean isolines in two different genetic background at three different seed weight stages: Seed coats of Clark standard (CS, wild type) & Clark defective (CD, seed coat mutant), Harosoy Standard (HS) & Harosoy defective (HD) at 50-100mg, 100-200mg and 400-500mg.

2014-05-16 | E-GEOD-54903 | biostudies-arrayexpress

IIdentification of GmLMM1-interacting protein in Arabidopsis

Project description:GmLMM1-FLAG was expressed in Arabidopsis protoplasts and GmLMM1-interacting protein was identified byprotein immunoprecipitation and mass spectrometric analysis

2020-08-31 | PXD020233 | Pride

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