GEO DataSets

(Submitter supplied) ChIP-seq was carried out with H3K4me3 antibody using Stem differentiating xylem from wild-type plants under drought conditions

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). more...

Organism:

Laccaria bicolor; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30192 GPL30193

60 Samples

Download data: TXT

(Submitter supplied) The plant xylem tissue is responsible for water transportation, mechanical support and lateral growth, and can be utilized as wood. The seed plant xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells, including tracheids in gymnosperms and vessel elements and libriform fibers in angiosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. more...

Organism:

Trochodendron aralioides; Eucalyptus grandis; Liriodendron chinense; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

6 related Platforms

48 Samples

Download data: CSV, H5, TAR, TXT

(Submitter supplied) ChIP-seq was carried out with FLAG antibody using stem cambium tissues from PtrVCS2-FLAG overexpression plants

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

6 Samples

Download data: BW, NARROWPEAK

(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; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26322

85 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26322

15 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26322

45 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL26322

10 Samples

Download data: TSV

(Submitter supplied) This research uses terminal branches from a wild poplar tree to track somatic genetic, epigenetic, and transcriptional changes. Using a multi-omics approach, we aim to identify and describe mutations which arise during the lifetime of a long-lived perennial plant.

Organism:

Populus trichocarpa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26322

15 Samples

Download data: TSV

(Submitter supplied) PtrHSFB3-1 and PtrMYB092 are xylem specific genes in xylem of P. trichocarpa, and their expression levels are down regulated most significantly in tension wood. These two transcription factors were transiently overexpressed in stem differentiating xylem (SDX) of P. trichocarpa , and transcriptomic sequencing was performed to identify the regulatory effects of the two transcription factors on wood formation related genes.

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23263

9 Samples

Download data: XLS

(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

(Submitter supplied) We studied the changes that occur in gene transcription during seasonal senescence in Populus trichocarpa pioneer leaves and fine roots. Plant senescence is a strictly regulated physiological process that allows relocating of valuable nutrients from senescent tissues before death. It might be induced by internal or external factors and among them, phytohormones play an undoubtedly significant role. Senescence was extensively studied in leaves, but the aging of other ephemeral organs, located underground, and its drivers are still poorly understood. We focused on collective results to fill in the knowledge gap about senescence of fine, absorptive roots and leaves in order to check if there are universal mechanisms involved during plant organ senescence. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in developmental PCD. Samples were collected three times during a growth season. The first collection was considered as a control and was collected in early summer (July 7–15) when leaves and the root system were fully developed and functional. The second group of leaf and root samples were harvested in early autumn (October 1–7) when chlorophyll levels in leaves had decreased by approximately 40% and when fine roots had changed in color from white to brown. The third group of samples were harvested in the middle of autumn (November 2–9) when chlorophyll levels in leaves decreased by approximately 65% and fine roots were dark brown or black color. Our results reveal the important role of phytohormones in regulating the senescence of both studied organs. The transcriptomic analyses showed significant changes in gene expression that are associated with phytohormones, especially with ABA and jasmonates. We conclude that phytohormonal regulation of senescence in roots and leaves is organ-specific. In roots, phytohormones are involved indirectly in regulation of senescence by increasing tolerance for cold or resistance for pathogens, whereas such correlation was not observed in leaves.

Organism:

Populus trichocarpa; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

18 Samples

Download data: CEL

(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

(Submitter supplied) We studied the changes that occur in gene transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in xylem formation. Pioneer roots were examined in segments corresponding to their developmental stage: apical meristem (PR1), primary development (PR2), and secondary development (PR3). more...

Organism:

Populus trichocarpa; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

18 Samples

Download data: CEL

(Submitter supplied) Chromatin accessibility and modification is a hallmark of regulatory DNA, which has led to the discovery of cis-regulatory elements (CREs). Here, we characterize chromatin accessibility, histone modifications and sequence conservation in 13 plant species. We identified thousands of putative CREs and revealed that distal CREs are prevalent in plants especially in species with large and complex genomes. more...

Organism:

Oryza sativa; Brachypodium distachyon; Arabidopsis thaliana; Phaseolus vulgaris; Sorghum bicolor; Zea mays; Spirodela polyrhiza; Populus trichocarpa; Glycine max; Hordeum vulgare; Setaria viridis; Asparagus officinalis; Eutrema salsugineum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

13 related Platforms

170 Samples

Download data: BW

(Submitter supplied) Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. more...

Organism:

Populus trichocarpa; Populus deltoides

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL25334 GPL25333

18 Samples

Download data: FA, TXT

(Submitter supplied) In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . more...

Organism:

Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23263

28 Samples

Download data: TXT

(Submitter supplied) We identified 1251 and 1509 significantly up-regulated and down-regulated genes, respectively (FDR<0.05) by drought-treatment. In contrast, in response to salt stress, only 133 genes and 309 genes were significantly up- and down-regulated (FDR<0.05) respectively. Of these, 55% of the up-regulated and 75% of the down-regulated genes were also identified in the drought data set.

Organism:

Populus trichocarpa; Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

9 Samples

Download data: CEL

(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

(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