GEO DataSets

(Submitter supplied) More then 10 million raw reads were acquired. In total, 238 unique mature sequences which contain 142 conserved miRNA and 96 novel miRNAs were identified.

Organism:

Populus euphratica

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24346

9 Samples

Download data: FA, TXT

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

Organism:

Populus euphratica

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24346

18 Samples

Download data: TXT

(Submitter supplied) More then 10 million raw reads were acquiredIn total, 247 unique mature sequences which contain 149 conserved miRNA and 98 novel miRNAs were identified.

Organism:

Populus euphratica

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL24346

9 Samples

Download data: FA, TXT

(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 sp.; Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL4359

18 Samples

Download data: CEL

(Submitter supplied) We present an efficient method to genome-wide discover new and drought stress responsive miRNAs in P. euphratica. High throughput sequencing of P. euphratica leaves found 197 conserved miRNAs between P. euphratica and Populus trichocarpa. Meanwhile, 189 new miRNAs which belonged to 120 families were identified, a large increasing to the number of P. euphratica miRNAs. Target prediction and degradome sequencing verification of 22 new and 21 conserved miRNA targets showed these targets were involved in multiple biological processes, including transcription regulation and response to stimulus. more...

Organism:

Populus euphratica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11262

2 Samples

Download data: FASTA, TXT

(Submitter supplied) We studied expression in roots of transgenic poplar (7171B4 genotype) plants expressing PcGA2ox1 or rgl1 under 35S promoter. Dwarf, semidwarf, wt-like and wt plants were used.

Organism:

Populus sp.

Type:

Expression profiling by array

Platform:

GPL4359

12 Samples

Download data: CEL

(Submitter supplied) In order to study the improtance of HSFA6b in salt and heat stresses of arabidopsis, we generated the HSFA6b-overexpression (HSFA6b-OE) and dominant-negative (HSFA6b-RD) mutant lines. We used microarray to investigate how genes regulated by HSFA6b after NaCl or heat shock treatment.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL, TXT

(Submitter supplied) In this study, C. gigantea miRNAs and their target genes were investigated by extracting RNA from young roots, tender stems, young leaves, and flower buds of C. gigantea to establish a small RNA (sRNA) library and a degradome library to further sequence. This study identified 194 known miRNAs belonging to 52 miRNA families and 23 novel miRNAs. Among the miRNA families, 158 miRNAs from 27 miRNA families were highly conserved and existed in a plurality of plants. more...

Organism:

Cercis gigantea (nom. inval.)

Type:

Non-coding RNA profiling by high throughput sequencing; Other

Platforms:

GPL19878 GPL19879

2 Samples

Download data: TXT

(Submitter supplied) Background: A long juvenile period between germination and flowering is a common characteristic among fruit trees, including Malus hupehensis (Pamp.) Rehd., which is an apple rootstock widely used in China. microRNAs (miRNAs) play an important role in the regulation of phase transition and reproductive growth processes. Results: M. hupehensis RNA libraries, one adult and one juvenile phase, were constructed using tree leaves and underwent high-throughput sequencing. more...

Organism:

Malus hupehensis

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL19425 GPL19426

3 Samples

Download data: TXT

(Submitter supplied) We aimed to identify putative ABA-regulated miRNAs expressed in rice by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from Osaba1-1 and wild type rice leaves, and more than ten million small RNA sequence reads were generated for each library. We identified 13 ABA-regulated miRNAs via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. more...

Organism:

Oryza sativa Japonica Group

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13834

2 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

Other; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

28 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Other

Platform:

GPL13160

4 Samples

Download data: TXT

(Submitter supplied) Elicitor-responsive miRNAs and their targets in rice

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13160

24 Samples

Download data: TXT

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

Organism:

Populus euphratica

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25640

24 Samples

Download data: TXT

(Submitter supplied) The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn from young to adult trees. It is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophyll, the juvenile heterophyll were respectively sampled, and then their expression patterns were analyzed by small RNA sequencing and strand-specific RNA sequencing. more...

Organism:

Populus euphratica

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25640

12 Samples

Download data: TXT

(Submitter supplied) The desert plant Populus euphratica Oliv. has typical heterophylly; linear (Li), lanceolate (La), ovate (Ov) and broad-ovate (Bo) leaves grow in turn from young to adult trees. It is therefore a potential model organism for leaf development. To investigate the roles of RNAs (including mRNAs, miRNAs, lncRNAs and circRNAs) in the morphogenesis of P. euphratica heterophyll, the juvenile heterophyll were respectively sampled, and then their expression patterns were analyzed by small RNA sequencing and strand-specific RNA sequencing. more...

Organism:

Populus euphratica

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL25640

12 Samples

Download data: 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) Plant material for EST library construction: The Ein Avdat valley is located in the Negev desert in Israel at 450 m above sea level and a latitude of 30° 49' 30" N, and a longitude of 34° 46' 0" E. The average rainfall is 100 to 200 mm per year with most of the rain falling during winter time. Adult heart shaped leaves were collected from trees in areas A, B, and C for the cDNA library during the summer seasons of 2000 to 2001. more...

Organism:

Populus euphratica

2 Series

6 Samples

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(Submitter supplied) Background: The change from juvenile to mature phase in woody plants is often accompanied by a gradual loss of rooting ability, as well as by reduced microRNA (miR) 156 and increased miR172 expression. Results: We characterized the population of miRNAs of Eucalyptus grandis and compared by Northern blot the gradual reduction in miR156 and increase in miR172 expression during development to the loss of rooting ability. more...

Organism:

Eucalyptus grandis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL18777

1 Sample

Download data: TXT

(Submitter supplied) Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid (SA), and indole-3-acetic acid conjugated with aspartic acid (IAAsp) on tuberous root development. more...

Organism:

Manihot esculenta

Type:

Expression profiling by array

Platform:

GPL22197

42 Samples

Download data: TXT