GEO DataSets

(Submitter supplied) Comparative analysis of nascent transcription among plant species

Organism:

Arabidopsis thaliana; Physcomitrium patens; Hordeum vulgare; Drosophila melanogaster; Selaginella moellendorffii; Carica papaya; Chlamydomonas reinhardtii; Zea mays

Type:

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

17 related Platforms

68 Samples

Download data: BED, TXT, XLSX

(Submitter supplied) To investigate global gene expression during meiosis in S. moellendorfii, digital gene-expression profiling of a series of sporangia at different developmental stages was performed by Illumina HiSeq™ 2000 sequencing platforms, with young leaves being used as a control. The samples were collected from South Mountain, Chongqing (29°33'44.18"N; 106°37'35.62"E) and stored in RNAlater solution. Total RNAs were extracted using the TRIzol solution. more...

Organism:

Selaginella moellendorffii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19601

7 Samples

Download data: FA, TXT

(Submitter supplied) RNA-seq expression data was generated for root, shoot, rhizophore, and leaf of S. moellendorffii.

Organism:

Selaginella moellendorffii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23399

8 Samples

Download data: XLSX

(Submitter supplied) Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. more...

Organism:

Psilotum nudum; Cibotium barometz; Asplenium nidus; Salvinia cucullata; Azolla caroliniana; Palhinhaea cernua; Selaginella moellendorffii; Plenasium vachellii; Microsorum cuspidatum; Equisetum ramosissimum; Cyrtomium fortunei; Angiopteris fokiensis; Diplopterygium chinense; Diplazium esculentum; Ophioglossum vulgatum; Isoetes sinensis; Dicranopteris pedata; Microlepia platyphylla; Salvinia molesta; Selaginella uncinata; Pteris vittata; Lygodium japonicum; Trichomanes striatum; Odontosoria chinensis; Alsophila spinulosa

Type:

Non-coding RNA profiling by high throughput sequencing

25 related Platforms

26 Samples

Download data: FASTA

(Submitter supplied) We define genome-wide temporal expression patterns of root development genes in seven vascular plants, enabling a detailed comparative analysis of the molecular development of a single organ across diverse species.

Organism:

Zea mays; Cucumis sativus; Arabidopsis thaliana; Solanum lycopersicum; Selaginella moellendorffii; Glycine max; Oryza sativa

Type:

Expression profiling by high throughput sequencing

7 related Platforms

60 Samples

Download data: CSV

(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; Pinus taeda; Arabidopsis thaliana; Solanum lycopersicum; Sorghum bicolor; Vitis vinifera; Physcomitrium patens; Triticum aestivum; Zea mays; Gossypium hirsutum; Brassica napus; Oryza sativa; Saccharum officinarum

Type:

Non-coding RNA profiling by array

Platform:

GPL9858

2 Samples

Download data: TXT

(Submitter supplied) Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and little is known about methylation outside of mammals, Arabidopsis thaliana, and Neurospora crassa. Utilizing deep bisulfite sequencing, we have quantified DNA methylation in five plant, seven animal, and five fungal genomes. We find that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons has evolved independently in the vertebrate lineage. more...

Organism:

Volvox carteri; Coprinopsis cinerea; Bombyx mori; Oryza sativa; Tribolium castaneum; Nematostella vectensis; Ciona intestinalis; Tetraodon nigroviridis; Chlorella variabilis; Physcomitrium patens; Phycomyces blakesleeanus; Drosophila melanogaster; Apis mellifera; Laccaria bicolor; Uncinocarpus reesii; Selaginella moellendorffii; Postia placenta

Type:

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

17 related Platforms

33 Samples

Download data: GFF, TXT

(Submitter supplied) The objective of this study was to identify nutrient-responsive small RNAs in different tissues and in phloem sap of rape plants. miRNA microarrays containing all currently known plant miRNAs (Sanger miRBase versions 10.0, 10.1 and 11.0), and a set of unknown small RNAs cloned earlier from Brassica phloem sap (Bn_PsRNA) were used. The phloem, leaf and root response to nutrient deficiency were analyzed by removing either sulfate, copper or iron from the growth medium. more...

Organism:

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

Type:

Non-coding RNA profiling by array

Platforms:

GPL9737 GPL9736 GPL9738

10 Samples

Download data: TXT

(Submitter supplied) The small RNAs of Selaginella moellendorffii were sampled by direct pyrosequencing (454 Life Sciences). These data represent microRNAs, siRNAs, and other expressed small RNAs of ~18-~28 nts. in length. Keywords: Small RNA sequencing - high throughput

Organism:

Selaginella moellendorffii

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL5014

1 Sample

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(Submitter supplied) LC Sciences provides a genome-wide microRNA (miRNA) expression profiling service using µParaflo® technology and proprietary probe design, which enable highly sensitive and specific direct detection of miRNAs. They have standard arrays for mature miRNA of all species available in the latest version of the Sanger miRBase database. A proprietary µParaflo® microfluidic chip is used. The microfluidic technology produces a uniform distribution of the sample solutions on the array and enhances binding reactions and stringency wash processes. more...

Organism:

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

1 Series

2 Samples

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(Submitter supplied) Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 11.0 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs) Protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. more...

Organism:

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

1 Series

3 Samples

Download data: TXT

(Submitter supplied) Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.1 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs) Protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. more...

Organism:

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

1 Series

4 Samples

Download data: TXT

(Submitter supplied) Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 10.0 and additional custom small RNA sequences from Brassica napus phloem sap (Bn_PsRNAs) Protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. more...

Organism:

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

1 Series

3 Samples

Download data: TXT

(Submitter supplied) Plant miRNA microarray with 100% coverage of mature miRNAs listed in miRBase version 14 Protocol: Arrays are made based µParaflo microfluidic technology (Atactic Technologies). On the µParaflo microfluidic chip, each detection probe consists of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. more...

Organism:

Chlamydomonas reinhardtii; Physcomitrium patens; Pinus taeda; Gossypium hirsutum; Populus trichocarpa; Arabidopsis thaliana; Brassica napus; Brassica rapa; Brassica oleracea; Malus domestica; Glycine max; Medicago truncatula; Phaseolus vulgaris; Solanum lycopersicum; Oryza sativa; Saccharum officinarum; Sorghum bicolor; Triticum aestivum; Zea mays; Brachypodium distachyon; Vitis vinifera; Populus euphratica; Selaginella moellendorffii; Aquilegia coerulea

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(Submitter supplied) Pyrosequencing of small RNAs from the lycopod Selaginella moellendorffii.

Organism:

Selaginella moellendorffii

1 Series

1 Sample

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