GEO DataSets

(Submitter supplied) The transition of axillary grapevine buds from paradormancy to endodormancy is an important mechanism for winter survival. Maintenance of paradormancy and transition to endodormancy may be synchronized by factors including phytohormones, genes, transcription factors and other molecular regulators. In the present study we used age matched buds from vines subjected to 28 days of short day (SD; 13h) treatment or continued long day (LD; 15h) photoperiod for high throughput transcriptome profiling.

Organism:

Vitis riparia

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23121

6 Samples

Download data: TXT

(Submitter supplied) Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long (15h) and short (13h) photoperiod. Three separate replicates (5 plants/replicate) were treated to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. Potted, spur-pruned two to six-year-old vines were removed from cold storage (Seyval 3-19-07; V. more...

Organism:

Vitis vinifera; Vitis hybrid cultivar; Vitis riparia

Type:

Expression profiling by array

Platform:

GPL1320

84 Samples

Download data: CEL

(Submitter supplied) We investigated differential gene expression patterns in Populus vegetative buds between paradormant, endodormant, and ecodormant dormancy states. Our primary objectives were to (1) identify which individual genes, biological processes, molecular functions, and regulatory pathways were differentially expressed among dormancy states, (2) classify the differentially expressed genes into contrasting gene expression patterns, and (3) identify cis-acting elements associated with each gene expression group. more...

Organism:

Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL20616

10 Samples

Download data: PAIR

(Submitter supplied) Buds were collected at equivalent branch positions and always at the same time of the day. Samples corresponding to May (MAY), June (JUN), July (JUL), September (SEP), November (NOV), January (JAN), March (MAR) and April (APR) buds were analyzed. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Jose Diaz-Riquelme. The equivalent experiment is VV36 at PLEXdb.]

Organism:

Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL11004

24 Samples

Download data: CEL

(Submitter supplied) Bud endodormancy induction response of two genotypes (‘Seyval’ a hybrid white wine grape and V. riparia, PI588259 a native north american species) was compared under long and short photoperiod. Three separate replicates (5 plants/replicate) were treated in each of 2 separate years (2007 and 2008) to generate paradormant (LD) and same aged endodormancy-induced (SD) buds for transcriptomic, proteomic and metabolomic analysis. more...

Organism:

Vitis riparia; Vitis vinifera; Vitis hybrid cultivar

Type:

Expression profiling by array

Platform:

GPL1320

167 Samples

Download data: CEL

(Submitter supplied) Leafy spurge is a model for studying well-defined phases of dormancy in underground adventitious buds (UABs) of herbaceous perennial weeds, which is a primary factor allowing many invasive perennial weeds to escape conventional control measures. A 12-week ramp down in both temperature (27°C → 10°C) and photoperiod (16 h → 8 h light) is required to induce a transition from para- to endo-dormancy in UABs of leafy spurge. more...

Organism:

Manihot esculenta; Euphorbia esula

Type:

Expression profiling by array

Platform:

GPL4655

84 Samples

Download data: GPR

(Submitter supplied) We used Illumina RNA-Seq technology to carry out digital gene expression profiling of Dormant and non dormant buds of Shine Muscat Cultivar.127 pathways were annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and metabolic, biosynthesis of secondry metabolite and. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were involved in various metabolic processes, including phytohormone metabolism. more...

Organism:

Vitis vinifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18740

3 Samples

Download data: TXT

(Submitter supplied) This study investigated changes in gene expression of controlled environment chilled (4C) grape overwintering buds as they accumulated from 0 to 2000 chilling hours. Keywords: time course, chilling, endodormancy release, axillary bud, grape

Organism:

Vitis riparia; Vitis vinifera

Type:

Expression profiling by array

Platform:

GPL6275

15 Samples

Download data: TXT

(Submitter supplied) Bud dormancy is a crucial stage in perennial trees and allows survival over winter and optimal subsequent flowering and fruit production. Environmental conditions, and in particular temperature, have been shown to influence bud dormancy. Recent work highlighted some physiological and molecular events happening during bud dormancy in trees. However, we still lack a global understanding of transcriptional changes happening during bud dormancy. more...

Organism:

Prunus avium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26587

82 Samples

Download data: TXT

(Submitter supplied) Genetic and epigenetic regulations, mostly driven by small non-coding RNAs, play a crucial role to define genetic programming in plant biology and development. In this work, we focus on miRNAs, the most representative class of small RNAs, to present the first comprehensive miRNA expression atlas in Vitis vinifera L. Our atlas gives a clear picture of miRNA regulation and homeostasis in the whole plant during its lifecycle. more...

Organism:

Vitis vinifera

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL18740 GPL15528

70 Samples

Download data: TXT

(Submitter supplied) Leafy spurge (Euphorbia esula) is an herbaceous perennial weed that produces vegetatively from an abundance of underground adventitious buds. The objectives of this study were to determine how mimicking natural seasonal conditions (photoperiod and temperature) under controlled environmental conditions affect dormancy and flowering competence; to determine molecular mechanisms associated with well-defined phases of seasonal dormancy transitions based on transcript profiles obtained by microarray analysis; and to link mechanisms regulating induction and release of endodormancy and flowering competence. more...

Organism:

Manihot esculenta; Euphorbia esula

Type:

Expression profiling by array

Platform:

GPL4655

32 Samples

Download data: GPR

(Submitter supplied) miRNA played an important role in the process of carcinogenesis in HBV related hepatocellular carcinoma. Therefore, we performed miRNA microarray to evaluate the miRNAs that expressed differentially between HCC tumor versus non-tumor liver tissues.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL10850

10 Samples

Download data: TXT

(Submitter supplied) Due to the broad climate adaptation of perennial trees, phenological traits (e.g. chilling requirement-CR, bloom date-BD) exhibit complex inheritance patterns. Conceptually, these are adaptive responses to abiotic stress. As production depends on traits like CR, breeders have developed varieties that are phenotypically/genotypically matched to particular geographic/temperature zones. These genotypes are ideal for study of gene networks governing these climate-critical traits. more...

Organism:

Prunus persica; Prunus armeniaca

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21993 GPL27604

129 Samples

Download data: TXT

(Submitter supplied) Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by abnormalities in reciprocal social interactions and language development and/or usage, and by restricted interests and repetitive behaviors. Differential gene expression of neurologically relevant genes in lymphoblastoid cell lines from monozygotic twins discordant in diagnosis or severity of autism suggested that epigenetic factors such as DNA methylation or microRNAs (miRNAs) may be involved in ASD. more...

Organism:

Homo sapiens; Rattus norvegicus; Mus musculus

Type:

Non-coding RNA profiling by array

Platform:

GPL10254

14 Samples

Download data: TXT

(Submitter supplied) Despite the identification of numerous autism susceptibility genes, the pathobiology of autism remains unknown. The present “case-control” study takes a global approach to understanding the molecular basis of autism spectrum disorders based upon large-scale gene expression profiling. DNA microarray analyses were conducted on lymphoblastoid cell lines from over 20 sib pairs in which one sibling had a diagnosis of autism and the other was not affected in order to identify biochemical and signaling pathways which are differentially regulated in cells from autistic and nonautistic siblings. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3427

38 Samples

Download data: MEV

(Submitter supplied) Background: The autism spectrum includes a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills, and are associated with odd, stereotyped, repetitive behavior and restricted interests. To date, diagnosis of these neurologically based disorders relies predominantly upon behavioral observations often prompted by delayed speech or aberrant behavior, and there are no known genes that can serve as definitive biomarkers for the disorders. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL3427

19 Samples

Download data