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Items: 14

1.

RNAseq of bending treated Populus trichocarpa

(Submitter supplied) We treated 6 month Populus trichocarpa by bending for 0, 3, and 7 days to see effects of bending treatment on wood formation at transcript level
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17415
9 Samples
Download data: XLS
Series
Accession:
GSE153793
ID:
200153793

PubMed Full text in PMC Similar studies SRA Run Selector

2.

Incidence of phosphate variations on nutrient transports in a symbiocosm formed by poplar, sorghum and Rhizophagus irregularis.

(Submitter supplied) We analyzed the impact of different phosphate levels on the regulation of plant and fungal transcriptomes.
Organism:
Populus trichocarpa; Rhizophagus irregularis; Sorghum bicolor
Type:
Expression profiling by high throughput sequencing
5 related Platforms
27 Samples
Download data: CSV, TXT
Series
Accession:
GSE138316
ID:
200138316

PubMed Full text in PMC Similar studies

3.

Integrative analysis of genome-wide histone H3 lysine 9 acetylation and gene expression in *Populus trichocarpa* under drought stress reveals that AREB1 transcription factors recruit the GCN5-ADA2b complexes to activate drought-inducible gene expression

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17415
24 Samples
Download data
Series
Accession:
GSE81048
ID:
200081048

PubMed Full text in PMC Similar studies

4.

Genome-wide analysis of histone H3 lysine 9 acetylation in Populus trichocarpa under drought stress

(Submitter supplied) We report on the genome-wide distribution pattern of histone H3 lysine 9 acetylation (H3K9ac) and the pattern’s association with whole genome expression profiles in Populus trichocarpa subjected to soil-water depletion. We identified a set of drought responsive genes whose expression is directly regulated by differential modification of H3K9ac.
Organism:
Populus trichocarpa
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL17415
12 Samples
Download data: TXT
Series
Accession:
GSE81047
ID:
200081047

PubMed Full text in PMC Similar studies SRA Run Selector

5.

RNAseq of drought treated Populus trichocarpa

(Submitter supplied) To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. more...
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17415
12 Samples
Download data: XLSX
Series
Accession:
GSE79401
ID:
200079401

PubMed Full text in PMC Similar studies SRA Run Selector

6.

Genome-wide investigation of pentatricopeptide repeat (PPR) gene family in poplar and their expression analysis in response to biotic and abiotic stresses

(Submitter supplied) Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30-40 amino acid sequence motifs, constitute a large gene family in plants. These known PPR proteins have been identified to play important roles in organellar RNA metabolism and plant development in Arabidopsis and rice. However, functions of PPR genes in woody species remain still largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the poplar genome. more...
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17415
7 Samples
Download data: XLS
Series
Accession:
GSE109609
ID:
200109609

PubMed Full text in PMC Similar studies SRA Run Selector

7.

Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

(Submitter supplied) Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.
Organism:
Laccaria bicolor; Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21175 GPL17415
2 Samples
Download data: TXT
Series
Accession:
GSE75437
ID:
200075437

PubMed Full text in PMC Similar studies SRA Run Selector

8.

RNA-seq of major tissues and xylem cell types of Populus trichocarpa

(Submitter supplied) We used the stem cross-sections of P. trichocarpa and our recently developed laser capture microdissection (LCM) to collect fibers, vessels, and a combination of 3 cell types (fibers + vessels + rays). Total RNA from the three samples was isolated, amplified, and analyzed by full-transcriptome RNA-sequencing. The sequencing reads were mapped to the P. trichocarpa genome.
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17415
24 Samples
Download data: TXT
Series
Accession:
GSE81077
ID:
200081077

PubMed Full text in PMC Similar studies SRA Run Selector

9.

Widespread natural variation of DNA methylation within angiosperms

(Submitter supplied) DNA methylation is a chemical modification of DNA that can be faithfully inherited across generations in flowering plant genomes. Failure to properly maintain DNA methylation can lead to epigenetic variation and transposon reactivation. Plant genomes are dynamic, spanning large ranges in size and there is an interplay between the genome and epigenome in shaping one another. To understand the variation in genomic patterning of DNA methylation between species, we compared methylomes of numerous diverse angiosperm species. more...
Organism:
Cannabis sativa; Cucumis sativus; Prunus persica; Manihot esculenta; Panicum virgatum; Fragaria vesca; Eucalyptus grandis; Medicago truncatula; Setaria viridis; Sorghum bicolor; Vitis vinifera; Theobroma cacao; Brassica rapa; Malus domestica; Ricinus communis; Brachypodium distachyon; Lotus japonicus; Citrus x clementina; Populus trichocarpa; Erythranthe guttata; Eutrema salsugineum; Beta vulgaris; Panicum hallii
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
30 related Platforms
34 Samples
Download data: TSV
Series
Accession:
GSE79526
ID:
200079526

PubMed Full text in PMC Similar studies SRA Run Selector

10.

FASTmC: predictive models for non-reference-based estimations of DNA methylation

(Submitter supplied) We describe a suite of predictive models, coined FASTmC, for non-reference, cost-effective exploration and comparative analysis of context-specific DNA methylation levels. Accurate estimations of true DNA methylation levels can be obtained from as few as several thousand short-reads generated from whole genome bisulfite sequencing. Our models make high-resolution time course or developmental, and large diversity studies practical regardless of species, genome size and availability of a reference genome.
Organism:
Populus trichocarpa; Brassica oleracea; Erythranthe guttata; Brachypodium distachyon; Sorghum bicolor
Type:
Methylation profiling by high throughput sequencing
5 related Platforms
5 Samples
Download data: TSV
Series
Accession:
GSE72155
ID:
200072155

PubMed Full text in PMC Similar studies SRA Run Selector

11.

RNAseq of xylem tissue of transgenic and wildtype Populus trichocarpa (NSF Plant Genome Research Program Project 0922391)

(Submitter supplied) We transformed Populus trichocarpa and generated transgenics with knockdown or overexpression of monolignol genes and transcription factors
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL17415 GPL17579
378 Samples
Download data: TXT
Series
Accession:
GSE78953
ID:
200078953

PubMed Full text in PMC Similar studies SRA Run Selector

12.

Single-base-resolution Methylomes of Populus trichocarpa Reveal the Association between DNA Methylation and Drought Tolerance

(Submitter supplied) DNA methylation is an important biological form of epigenetic modification, playing key roles in plant development and environmental responses. In this study, we examined single-base resolution methylomes of Populus under control and drought stress conditions using high-throughput bisulfite sequencing for the first time. Our data showed methylation levels of methylated cytosines, upstream2kp, downstream2kb, and repeatitive sequences significantly increased after drought treatment in Populus. more...
Organism:
Populus trichocarpa
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL17415
2 Samples
Download data: TXT
Series
Accession:
GSE55087
ID:
200055087

SRA Run Selector

13.

A comprehensive survey of degradation and 3′ end modification of plant microRNAs by deep sequencing

(Submitter supplied) The degradation and 3′ end modification of plant microRNAs (miRNAs) play crucial roles in regulating miRNA function and stability. However, the process and mechanism of miRNA degradation and 3′ end modification has, to date, been poorly characterized. Here, we report that analysis of the two small RNA libraries constructed from two hickory floral differentiation stages by deep sequencing obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. more...
Organism:
Populus trichocarpa
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL17415
2 Samples
Download data: TXT
Series
Accession:
GSE48584
ID:
200048584

SRA Run Selector

14.

Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa

(Submitter supplied) Laccases were proposed to catalyze the oxidative polymerization of monolignols. We identified 49 laccase gene models in Populus trichocarpa, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed Ptr-MIR397a in transgenic P. trichocarpa. In each of all 9 transgenic lines tested, 17 PtrLACs were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an approximately 40% decrease in the total laccase activity. more...
Organism:
Populus trichocarpa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17415
12 Samples
Download data: TXT
Series
Accession:
GSE54153
ID:
200054153

PubMed Full text in PMC Similar studies SRA Run Selector

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