GEO DataSets

(Submitter supplied) Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. more...

Organism:

Coffea canephora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26348

12 Samples

Download data: TXT

(Submitter supplied) The intermediate seed category was defined in the early 1990s using coffee (Coffea arabica) as a model. In contrast to orthodox seeds, intermediate seeds cannot survive complete drying, which is a major constraint for seed storage, for both biodiversity conservation and agricultural purposes. However, intermediate seeds are considerably more tolerant to drying than recalcitrant seeds, which are highly sensitive to desiccation. more...

Organism:

Coffea arabica

Type:

Expression profiling by array

Platform:

GPL24372

42 Samples

Download data: TXT

(Submitter supplied) SRNAs from field collected Coffea canephora leaves were profiled by Illumina sequencing and 63 unique microRNA genes belonging to 34 families were found.

Organism:

Coffea canephora

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17111

1 Sample

Download data: TXT

(Submitter supplied) Asterids is one of the major plant clades comprising of many commercially important medicinal species. One of the major concerns in medicinal plant industry is adulteration/contamination resulting from misidentification of herbal plants. This study reports the construction and validation of a microarray capable of fingerprinting medicinally important species from the Asterids clade.

Organism:

Codonopsis; Valeriana officinalis; Taraxacum officinale; Lonicera japonica; Lycium barbarum; Leonurus cardiaca; Embryophyta; Digitalis purpurea; Platycodon grandiflorus; Symphytum; Cornus; Achillea millefolium; Impatiens; Tetrapanax papyrifer; Scrophularia nodosa; Gardenia jasminoides; Forsythia suspensa; Withania somnifera; Ilex paraguariensis; Sambucus nigra; Camellia sinensis; Coffea arabica; Angelica archangelica; Vitex agnus-castus; Trachelospermum jasminoides; asterids; Rehmannia glutinosa

Type:

Genome variation profiling by array

Platform:

GPL14119

27 Samples

Download data: TXT

(Submitter supplied) Background: Understanding the genetic elements that contribute to key aspects of coffee biology will impact future agronomical improvements for this economically important tree. The past years, EST collections were generated in Coffee, opening the possibility to create new tools for functional genomics. Results: The project PUCE CAFE, set up by the scientific consortium NESTLE/IRD/CIRAD has developed of long oligonucleotide coffee array using public coffee EST sequences mainly obtained from different stages during fruit development and leaves in Coffea canephora (Robusta). more...

Organism:

Coffea arabica

Type:

Expression profiling by array

Platform:

GPL10928

18 Samples

Download data: TXT

(Submitter supplied) Background: Polyploidy has long been recognized as an important mechanism in eukaryotes evolution. Recent studies have documented dynamic changes in plant polyploid gene expression, which reflects genomic and functional plasticity of duplicate genes and genomes in plants. Genomewide approaches in a variety of allopolyploids, mostly synthetics, reveal a trend of non-additive gene expression. The aim of the study was to document expression divergence between a relatively recently formed natural allopolyploid (Coffea arabica) and its ancestral parents (Coffea canephora and Coffea eugenioides) and to verify if the divergence was ‘environment-dependent’.Results: Employing a microarray platform designed against 15,522 unigenes, we assayed gene expression levels in allopolyploid and its two parental diploids. more...

Organism:

Coffea arabica

Type:

Expression profiling by array

Platform:

GPL10928

72 Samples

Download data: TXT

(Submitter supplied) The closely related Coffea arabica cultivars ‘Tall Mokka’ and ‘Typica’, with excellent flavor, but differing distinctively in the size of aerial organs, branching pattern and branch numbers. Differential gene expression analysis of shoot tips of arabica coffee cultivars 'Tall Mokka' and 'Typica' were done using Potato cDNA microarray as cross-species platform. Using cross-species microarray hybridization, we identified a prolyl oligopeptidase (CaPOP) gene as differentially expressed between the shoot tips of ‘Tall Mokka’ and ‘Typica’. more...

Organism:

Solanum tuberosum; Coffea arabica

Type:

Expression profiling by array

Platform:

GPL14110

8 Samples

Download data: GPR

(Submitter supplied) Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). more...

Organism:

Coffea; Coffea hybrid cultivar

Type:

Expression profiling by array

Platform:

GPL1730

6 Samples

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(Submitter supplied) The Coffea Genome Oligo contains 15.580 70mers representing 15.580 genes. The Coffea canephora long oligonucleotide set was designed and synthetized by Operon (Town, State) based on the SGN Coffee built II (15721 unigenes; http://solgenomics.net/ ). An amino linker was attached to the 5'-end of each oligonucleotide. The oligonucleotides, selected to limit secondary structure, have a melting temperature of 67 ± 3°C, length 65 ± 5 bases, GC content 43 ± 5 %. more...

Organism:

Coffea arabica

1 Series

42 Samples

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(Submitter supplied) The Coffea Genome Oligo contains 15.580 70mers representing 15.580 genes. The Coffea canephora long oligonucleotide set was designed and synthetized by Operon (Town, State) based on the SGN Coffee built II (15721 unigenes; http://solgenomics.net/ ). An amino linker was attached to the 5'-end of each oligonucleotide. The oligonucleotides, selected to limit secondary structure, have a melting temperature of 67 ± 3°C, length 65 ± 5 bases, GC content 43 ± 5 %. more...

Organism:

Coffea arabica

2 Series

90 Samples

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(Submitter supplied) Nylon membranes containing coffee ESTs from subtracted cDNA librares. Plasmid clones were used. A set of sixteen 96-well plates was spotted on two nylon filters (85 mm x 125 mm) in a 4 x 4 array configuration, with a 96 pins hand-held array tool

Organism:

Coffea hybrid cultivar

1 Series

6 Samples

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