GEO DataSets

(Submitter supplied) Adventitious roots (AR) develop from tissues other than the primary root, in a developmental process physiologically regulated by phytohormones. Adventitious roots provide structural support and contribute to water and nutrient absorption, and are critical for commercial vegetative propagation of several crops. Here we quantified the number of AR, root architectural traits and root biomass in cuttings from a pseudo-backcross population of Populus deltoides and Populus trichocarpa. more...

Organism:

Populus trichocarpa x Populus deltoides; Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL20736

120 Samples

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(Submitter supplied) Adventitious root formation at the base of plant cuttings is an innate de novo organogenesis process that allows massive vegetative propagation of many economically and ecologically important species. The early molecular events following shoot excision are not well understood. Using whole-genome microarrays, we detected significant transcriptome remodeling during 48 hours following shoot removal in Populus softwood cuttings in the absence of exogenous auxin, with 27% and 36% of the gene models showing differential abundance between 0 and 6 hours, and 6 and 24 hours, respectively. more...

Organism:

Populus tremula x Populus alba; Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL7234

39 Samples

Download data: TXT

(Submitter supplied) Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction.

Organism:

Populus trichocarpa; Populus tremula x Populus tremuloides

Type:

Expression profiling by array

Platform:

GPL13485

27 Samples

Download data: PAIR

(Submitter supplied) Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. more...

Organism:

Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL2699

9 Samples

Download data: PAIR

(Submitter supplied) For the RNA-seq experiments approximately 3 cm stem segments were excised from 2-week-old in vitro plants and subsequently transfer to 1/2 MS medium and harvested the basal ends of stem cuttings (0.5 cm) at different time points(0, 0.5, 1, 2, 6, 12, 24, 48 and 96 h). Samples were collected from two biological replicates (40 cuttings each).

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25374

18 Samples

Download data: TXT

(Submitter supplied) We identified coherent type 4 feed-forward loops (FFLs) from this ML-hGRN, where PuHox52 repressed the expression of PuHDA9, which in turn augmented the histone H3K9 acetylation around the proximal regions of three direct target genes of PuHox52, PuWRKY51, PuLBD21 and PuIAA7, resulting in further enhanced expression levels of these target genes. Our study manifests evidence that supports a ML-hGRN with at least three coherent type 4 FFLs governed AR formation process at basal ends of stem cuttings in poplar.

Organism:

Populus ussuriensis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26876

8 Samples

Download data: BIGWIG

(Submitter supplied) RNA-seq was performed to examine the differential expressed transcriptomes with five-point experiment (6, 12, 24, 48 and 96 h) at the stem bases of cuttings in PuHox52 overexpression line compare to wild type Populus ussuriensis.

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25360

20 Samples

Download data: TXT

(Submitter supplied) To reveal transcriptome dynamics during adventitious root formation in a coniferous tree, C. japonica, we conducted custom microarry experiments. Three parts from cuttings of easy-to-root clone of C. japonica were collected at eight time points during adventitious root formation. The results revealed major turning points on transcriptome toward adventitious root formation and the expression behavior of genes related to carbohydrate, plant hormone and others suggested the important biological changes for adventitious root formation.

Organism:

Cryptomeria japonica

Type:

Expression profiling by array

Platform:

GPL21366

72 Samples

Download data: TXT

(Submitter supplied) Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of transgenic plants for most species. Our aims are to improve knowledge of gene regulatory circuits important to meristem organization, and to identify regulatory genes that might be useful for improving the efficiency of regeneration during transformation. We analyzed gene expression during poplar regeneration using an Affymetrix GeneChip® array representing over 56,000 poplar transcripts. more...

Organism:

Populus sp.; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL4359

10 Samples

Download data: CEL

(Submitter supplied) For RNA-seq, new cuttings from 3-week-old in vivo plants were cultured on the solid Woody Plant Medium (WPM) containing 20 g/L sucrose and 3 g/L Gelrite (Duchefa). After 5 days of culture, the root primordium formed cuttings were transferred to modified liquid WPM containing 10 μM or 200 μM KH2PO4, and harvested the basal ends of stem cuttings containing root primordium with its surrounding tissues using 11# scalpel after 2h, 4h, 8h, 12h and 24h culture. more...

Organism:

Populus ussuriensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25374

20 Samples

Download data: TXT

(Submitter supplied) Rooting capability is one of the economically traits lost during the juvenile to mature phase change in woody plants. A comprehensive microarray analysis was performed to compare the profiles of gene expression in juvenile and mature cuttings from E. grandis, either auxin treated or untreated on days, 0, 1, 3, 6, 9 and 12 post excision. At the end of the experiment, root primordia were observed only in auxin treated juvenile cuttings. more...

Organism:

Eucalyptus grandis

Type:

Expression profiling by array

Platform:

GPL18659

64 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Populus trichocarpa x Populus deltoides; Populus deltoides; Populus tremula x Populus alba; Populus euphratica; Populus trichocarpa

Type:

Expression profiling by array

Platforms:

GPL6032 GPL6596

12 Samples

Download data: GPR, TXT

(Submitter supplied) Populus deltoides and Populus trichocarpa were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure

Organism:

Populus trichocarpa; Populus euphratica; Populus deltoides

Type:

Expression profiling by array

Platform:

GPL6596

6 Samples

Download data: GPR, TXT

(Submitter supplied) Three tolerant and three sensitive genotypes of the inbred QTL mapping population Family 331 were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure

Organism:

Populus trichocarpa x Populus deltoides; Populus tremula x Populus alba; Populus euphratica

Type:

Expression profiling by array

Platform:

GPL6032

6 Samples

Download data: GPR, TXT

(Submitter supplied) Background Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. more...

Organism:

Populus sp.; Populus tremula

Type:

Expression profiling by array

Platform:

GPL4359

18 Samples

Download data: CEL

(Submitter supplied) In order to identify genes specifically induced during various developmental stages of Adventitious Root (AR) formation (described in Ahkami et al. 2009) in leafy cuttings of Petunia hybrida (line W115) and to describe the series of physiological processes during adventitious rooting, a microarray-based transcriptome analysis in the stem base of the cuttings was conducted. The microarray was described by Breuillin et al. more...

Organism:

Petunia x hybrida

Type:

Expression profiling by array

Platform:

GPL18705

28 Samples

Download data: TXT, XLS

(Submitter supplied) Strigolactone (SL) and auxin are two important phytohormones involved in plant root development, but whether they show synergistic or mutual promotion effects during adventitious root (AR) formation has not been adequately explored.

Organism:

Cucumis melo

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33469

9 Samples

Download data: TXT

(Submitter supplied) We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. more...

Organism:

Populus sp.; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL4359

26 Samples

Download data: CEL

(Submitter supplied) We study differences in gene expression between Populus P35S::BL (BL-oe) lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by overexpression of BL gene. We identified an activation tagging mutant with increased leaf size and correspondingly name it BIG LEAF (BL). more...

Organism:

Populus sp.; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL4359

12 Samples

Download data: CEL

(Submitter supplied) After four weeks the primary roots were cut off from the seedlings. The hypocotyl cuttings were treated in Hoagland nutrient solution at pH 5.8 containing 1.23 mM indole-3-butyric acid(IBA) for six hours then transferred to Hoagland nutrient solution lacking IBA. The hypocotyls were harvested at the following time points: day o,3,6,9,12 and 33. Keywords: time-course

Organism:

Pinus taeda; Pinus contorta

Type:

Expression profiling by array

Dataset:

GDS966

Platform:

GPL1014

29 Samples

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