GEO DataSets

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

Organism:

Brassica napus; Glycine max; Populus; Solanum tuberosum; Oryza sativa; Saccharum officinarum; Citrus sinensis; Zea mays; Dianthus caryophyllus; Arabidopsis thaliana; Solanum lycopersicum

Type:

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

11 related Platforms

160 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a powerful method for profiling histone modifications and transcription factors binding throughout the genome. However, its application in economically important plant organs (EIPOs) such as seeds, fruits, tubers and flowers is challenging due to their sturdy cell walls and complex constituents. Here, we present advanced ChIP (aChIP), an optimized ChIP-seq strategy that efficiently isolates chromatin from plant tissues while simultaneously removing plant cell walls and cellular constituents. more...

Organism:

Arabidopsis thaliana; Brassica napus; Solanum tuberosum; Saccharum officinarum; Citrus sinensis; Populus; Oryza sativa; Dianthus caryophyllus; Solanum lycopersicum; Zea mays; Glycine max

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

152 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) A field experiment was conducted at the Agricultural Sciences Center of the Federal University of Sao Carlos in Araras (22°21'25''S and 47°23'3''W) in the state of Sao Paulo, Brazil. Trial plots of SP-3280 consisted of four rows of 10 m long and spaced 1.35m apart. The field experiment was initiated in April 2012 and extended up until May 2013, representing the conditions under which one-year-and-a-half sugarcane crops are cultivated.

Organism:

Saccharum hybrid cultivar (mixed); Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

24 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of sugarcane leaf (+1) was collected from drought-prone areas at 42 and 117 days after the last rainfall when plants were 6- and 9-month-old, respectively. Sample hybridization (non-irrigated treatment against irrigated control) was performed to monitor gene expression in a two-color Agilent custom microarray. Our goal was to investigate the effect of mild and severe water stress on the transcriptomes of drought-sensitive (IACSP97-7065) and -tolerant (IACSP94-2094) sugarcane genotypes.

Organism:

Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL22278

10 Samples

Download data: TXT

(Submitter supplied) Microarrays using as samples leaves +1 of 4-month-old sugarcanes collected in winter. The 12 samples are in duplicates, collected every 2 h for 22h, starting 1.5 h before dawn. The microarray experiments are a time point against an equimolar pool of all samples, using as crossreference a dye-swap of the biological replicate collected at the same time point.

Organism:

Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL22278

24 Samples

Download data: TXT

(Submitter supplied) A field experiment was conducted at the Federal University of Alagoas in Maceio, Brazil. varieties RB86-7515, RB85-5536 and RB92-579 were distributed in a randomized block design with four replicates in two conditions: irrigated (control) and non-irrigated (treatment).

Organism:

Saccharum hybrid cultivar (mixed); Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

12 Samples

Download data: TXT

(Submitter supplied) A greenhouse experiment was conducted at the Federal University of Alagoas in Maceio, Brazil. One-eye sett of sugarcane was planted in 20 liters plant pots, arranged in a completely randomized design and cultivated for 5 months before water privation.

Organism:

Saccharum hybrid cultivar (mixed); Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

12 Samples

Download data: TXT

(Submitter supplied) To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single dose (SD) SNPs and 68,648 low dosage (33,277 SD and 35,371 double dose) SNPs from two datasets respectively were selected and tiled on Affymetrix Axiom SNP array. more...

Organism:

Saccharum officinarum

Type:

Genome variation profiling by SNP array

Platform:

GPL26249

471 Samples

Download data: CEL, TXT

(Submitter supplied) A field experiment was conducted at the Agricultural Sciences Center of the Federal University of Sao Carlos in Araras (22'21'25'S and 47'23'3'W) in the state of Sao Paulo, Brazil. Trial plots of SP-3280 consisted of four rows of 10 m long and spaced 1.35m apart. The field experiment was initiated in October 2012 and extended up until November 2013, representing the conditions under which ?one-year? sugarcane crops are cultivated.

Organism:

Saccharum hybrid cultivar (mixed); Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

30 Samples

Download data: TXT

(Submitter supplied) Sugarcane (Saccharum hybrid, SP80-3280) was grown in the field in Araras (Brazil) for 9 months. Leaves +1 (F1), internodes 1&2 (I1), and internodes 5 (I5) were harvested every 2 h for 26 h, starting 2h before dawn.

Organism:

Saccharum officinarum; Saccharum hybrid cultivar SP80-3280

Type:

Expression profiling by array

Platform:

GPL14862

84 Samples

Download data

(Submitter supplied) Transcriptional profile of sugarcane plants variety SP80-3280 inoculated with the pathogen Leifsonia xyli subsp. xyli (Lxx) compared with mocked inoculated ones 30 and 60 days after inoculation (DAI). Goal was to determine the effects of the increase in Lxx title on global sugarcane gene expression.

Organism:

Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

4 Samples

Download data

(Submitter supplied) Background: Sugarcane is an important sugar and energy crop largely used for bioethanol production in the world. The development of sugarcane cultivars with high sucrose content and yield is one of the biggest challenges of breeding programs nowadays. To identify genes networks that underlie sucrose content and yield, we used a custom designed oligonucleotide array with 21,901 different probes to study the transcriptome from breeding populations of sugarcane contrasting to sucrose content and genotypes contrasting to photosynthesis rate. more...

Organism:

Saccharum officinarum; Saccharum hybrid cultivar (mixed)

Type:

Expression profiling by array

Platform:

GPL14862

30 Samples

Download data

(Submitter supplied) Transcriptional profiling of sugarcane leaf+1 and upper internode harvested at one and five days after chemical (ethephon and AVG) application (DAA) compared to control (mock) samples. Co-hybridization of chemical-treated samples with control samples as reference (one or five DAA chemical treated-samples against one DAA control sample; and five DAA chemical treated-sample against five DAA control sample) was performed to monitor gene expression changes in a two-color Agilent custom microarray, using a dye-swap design. more...

Organism:

Saccharum officinarum; Saccharum sp.

Type:

Expression profiling by array

Platform:

GPL22278

24 Samples

Download data: TXT

(Submitter supplied) Sugarcane accumulates high concentrations of sucrose in the mature stalk, with numerous physiological processes in maturing stalk tissue both directly and indirectly involved. A considerable portion of carbohydrate metabolism is also devoted to cell wall synthesis and fibre production. Previously, we have identified differentially expressed transcripts correlated with sucrose accumulation and fibre production in various internodes of the sugarcane stalk. more...

Organism:

Saccharum officinarum; Saccharum hybrid cultivar Q117

Type:

Expression profiling by array

Platform:

GPL3844

9 Samples

Download data: CEL

(Submitter supplied) Sugarcane plants were grown in soil in a 12h light/ 12h dark photoperiod and 26oC for 3 months. Then, the plants were transferred to constant light conditions and 24 h later, leaves were harvested every 4 h for 48 h.

Organism:

Saccharum officinarum; Saccharum hybrid cultivar (mixed)

Type:

Expression profiling by array

Platform:

GPL14862

22 Samples

Download data

(Submitter supplied) Differential expression of microRNAs was studied in maize leaves after an 8-h-exposure under UV-B light. As a control, plants were kept in the greenhouse in the absence of UV-B

Organism:

Populus trichocarpa; Glycine max; Medicago truncatula; Selaginella moellendorffii; Physcomitrium patens; Triticum aestivum; Zea mays; Pinus taeda; Arabidopsis thaliana; Solanum lycopersicum; Sorghum bicolor; Vitis vinifera; Gossypium hirsutum; Brassica napus; Oryza sativa; Saccharum officinarum

Type:

Non-coding RNA profiling by array

Platform:

GPL9858

2 Samples

Download data: TXT

(Submitter supplied) Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. more...

Organism:

Saccharum officinarum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15137

2 Samples

Download data: TXT

(Submitter supplied) Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Regular watering was maintained for 90 days and suppressed after this period for the experimental group. Leaves were collected 24 h, 72 h and 120 h after exposure to drought conditions for the control and experimental groups. more...

Organism:

Saccharum hybrid cultivar (mixed); Saccharum officinarum

Type:

Expression profiling by array

Platform:

GPL14862

6 Samples

Download data

(Submitter supplied) Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. more...

Organism:

Saccharum officinarum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15137

1 Sample

Download data: TXT

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

Organism:

Physcomitrium patens; Zea mays; Danio rerio; Macaca mulatta; Pan troglodytes; Pongo pygmaeus; human gammaherpesvirus 4; Gallid alphaherpesvirus 2; Schmidtea mediterranea; Betapolyomavirus macacae; Populus trichocarpa; Glycine max; Medicago truncatula; Gallus gallus; Pan paniscus; Ovis aries; Murid gammaherpesvirus 4; Arabidopsis thaliana; Sorghum bicolor; Caenorhabditis briggsae; Caenorhabditis elegans; Anopheles gambiae; Drosophila melanogaster; Drosophila pseudoobscura; Apis mellifera; Xenopus laevis; Xenopus tropicalis; Ateles geoffroyi; Gorilla gorilla; Bos taurus; Mus musculus; Rattus norvegicus; Human gammaherpesvirus 8; Macacine gammaherpesvirus 4; Saguinus labiatus; Tetraodon nigroviridis; Oryza sativa; Saccharum officinarum; Bombyx mori; Lemur catta; Lagothrix lagotricha; Macaca nemestrina; Homo sapiens; Canis lupus familiaris; Sus scrofa; Human betaherpesvirus 5; Monodelphis domestica; Takifugu rubripes

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platforms:

GPL6844 GPL10558

16 Samples

Download data: GPR