GEO DataSets

(Submitter supplied) Analysis of gene expression of medicinal plants from different habitats is essential for quality control. This analysis completed the transcriptome sequencing of 12 samples of Angelicae Pubescentis Radix from four different habitats, and a total of 81.24 G CleanData was obtained. The effective data volume of each sample was distributed in 5.97 ~ 7.01 G, the Q30 base distribution was 93.81 ~ 94.67 %, and the average GC content was 42.5 %. more...

Organism:

Angelica pubescens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35350

12 Samples

Download data: FA, TXT

(Submitter supplied) Purpose:Next generation sequencing has been done to compare differrent transcriptome profiling between control groups and cold treated groups of Saposhnikovia divaricate (Turcz.) Schischk. Methods:Retinal mRNA profiles of 48d-old control samples (CK)and 6h/48h cold treated under 4°C were generated by deep sequencing, in triplicate, using Illumina NovaSeq 6000 Platform. Results: Using an optimized data analysis workflow, we obtained 6.1 GB of clean reads with an impressive Q30 percentage > 91.58%. more...

Organism:

Saposhnikovia divaricata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34866

9 Samples

Download data: XLS

(Submitter supplied) Plant growth-promoting rhizobacteria (PGPR) are soil microbes that can promote plant growth and/or increase plant resistance to one or multiple stress conditions. These natural resources are environmentally friendly tools for reducing the use of chemical fertilizers and pesticides and for improving the nutritional quality of plants, including pharmacological metabolites. Coriander (Coriandrum sativumL.), commonly known as cilantro or Chinese parsley, is a worldwide culinary and medicinal plant with both nutritional and medicinal properties. more...

Organism:

Coriandrum sativum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33916

6 Samples

Download data: TXT

(Submitter supplied) To test the impacts of drought on the host and fungus, we inoculated carrots (Daucus carota cv. ‘Napoli’) with spores of Rhizophagus irregularis DAOM 197198. Carrots grew in a greenhouse, and at the beginning of taproot development, were exposed to a 10-day water restriction. We evaluated plant growth and physiological responses, colonization level, and plant and fungal gene expression.

Organism:

Rhizophagus irregularis; Daucus carota

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL31010 GPL31009

16 Samples

Download data: TSV

(Submitter supplied) Effect of betanin synthesis on the metabolism of transgenic carrot. Betalain is a natural pigment with important nutritional value and broad application prospects. Previously, we produced betanin biosynthesis transgenic carrots via expressing optimized genes CYP76AD1S, cDOPA5GTS and DODA1S. Betanin can accumulate throughout the whole transgenic carrots. But the effects of betanin accumulation on the metabolism of transgenic plants and whether it produces unexpected effects are still unclear.

Organism:

Daucus carota

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33364

6 Samples

Download data: TXT

(Submitter supplied) To investigate the transcriptome changes by CO2 supply, we evaluated the transcriptional changes in fennel. We then performed gene expression profiling analysis using data obtained from RNA-seq of fennel at two stress conditions.

Organism:

Anethum foeniculum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32865

6 Samples

Download data: FASTA, TXT

(Submitter supplied) We provide a comparative transcriptomics analysis between wild (red or Delhi) and modified (orange or hybrid) carrot roots available in India.

Organism:

Daucus carota subsp. sativus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30383

2 Samples

Download data: FASTA, XLSX

(Submitter supplied) Purple carrots can accumulate large quantities of anthocyanins in their roots. Depending on the genetic background, anthocyanin pigmentation can be expressed in the entire root, or it can display tissue specific-patterns, confined to the root phloem or xylem tissues. Within the phloem, the tissue usually contributing most of the overall anthocyanin concentration in the carrot root, purple pigmentation can be found in the outer phloem (OP) (also called cortex) and inner phloem (IP) tissues, or it can be confined exclusively to the OP. more...

Organism:

Daucus carota

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30485

18 Samples

Download data: RESULTS

(Submitter supplied) The capability of the U.S. Food and Drug Administration Enteric Viruses tiling microarray (FDA-EVIR) was assessed for rapid molecular identification of human norovirus (NoV) and hepatitis A virus (HAV) extracted from artificially inoculated fresh produce. Two published viral extraction strategies, total RNA extraction or virus particle isolation, were employed to prepare the viral targets. We also assessed the amount of viral RNA extracted from celery by three commercially-available kits and how well that RNA performed on the FDA-EVIR. more...

Organism:

Bacillus subtilis; unidentified adenovirus; Hepatovirus A; Astrovirus sp.; Allium fistulosum; Apium graveolens; Solanum lycopersicum; Coxsackievirus; Sapovirus; Norovirus; Rotavirus; Paslahepevirus balayani

Type:

Expression profiling by genome tiling array

Platform:

GPL27751

17 Samples

Download data: CEL

(Submitter supplied) Taproots of different carrot genotypes were used to identify the candidate genes related to anthocyanin synthesis with particular focus on R2R3MYB, bHLH transcription factors, and glutathione S-transferase gene (GST). The RNA-sequencing analysis (RNA-Seq) showed that DcMYB6 and DcMYB7 had genotypic dependent expressed and they are likely involved in the regulation of anthocyanin biosynthesis. They were specifically upregulated in solid black taproots, including both black phloem and xylem. more...

Organism:

Daucus carota

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28229

10 Samples

Download data: TXT

(Submitter supplied) Cacao, spinach and carrot are three important crops with high valuable markets. For these species there isn't already an available genome-wide annotation of small rna. Here, for the first time, we sequenced and annotated small RNAs.

Organism:

Theobroma cacao; Daucus carota; Spinacia oleracea

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24089 GPL24090 GPL24091

5 Samples

Download data: TXT

(Submitter supplied) Glehnia littoralis is a perennial herb growing on the sandy beaches. In this study, high-throughput sequencing of small RNA was performed to identify miRNAs and their response to salt stress in G. littoralis. As a result, 37 conserved miRNAs belonging to 13 families and 37 novel miRNAs were identified. Among the 74 miRNAs, the expression levels of miR-156b*, miR-171, miR-171*, and miR-319 were downregulated and that of miR-399a, miR-399a*, miR-399b, miR-399b*, novel-9 and novel-14* were upregulated under salt stress. more...

Organism:

Glehnia littoralis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22174

3 Samples

Download data: TXT

(Submitter supplied) In this study, a cross species hybridization (CSH) approach was used to evaluate whole transcriptome changes during carotenoid accumulation in the storage root of carrot (Daucus carota). Carotenoids are isoprenoid compounds providing red, yellow and orange color to plants. Previous gene expression analyses of carotenoid accumulation in non-model plant species have primarily used a candidate gene approach. more...

Organism:

Medicago sativa; Medicago truncatula; Daucus carota; Sinorhizobium meliloti

Type:

Expression profiling by array

Platform:

GPL4652

6 Samples

Download data: CEL, CHP

(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:

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; Embryophyta; Digitalis purpurea; Platycodon grandiflorus; Symphytum; Codonopsis; Valeriana officinalis; Taraxacum officinale; Lonicera japonica; Lycium barbarum; Leonurus cardiaca

Type:

Genome variation profiling by array

Platform:

GPL14119

27 Samples

Download data: TXT

(Submitter supplied) Radix bupleuri is a traditional Chinese crude drug and it is still widely used in contemporary medicine. Bupleurum chinense DC. and B. scorzonerifolium Willd. are officially recorded as the source species of Radix bupleuri in Pharmacopoeia of the People’s Republic of China. The obvious difference in chemical active components and pharmacological action of Radix bupleuri derived from the two species has caused attention. more...

Organism:

Bupleurum scorzonerifolium; Bupleurum chinense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17771 GPL17772

2 Samples

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