GEO DataSets

(Submitter supplied) Nitrogen (N) can be absorbed by plants, thereby affects plant physiological activity, interferes gene expression, alters metabolite content and influences plant growth. However, the molecular mechanism underlying the potato tuberization response to nitrogen remains unclear. The plants were cultivated in the pots using N-deficient, N-Routine and N-sufficient conditions. Physiological response analysis, transcriptomics and metabolomics were performed on potato stolon exposed to Nitrogen stress. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

9 Samples

Download data: TXT

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

Organism:

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

Type:

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

11 related Platforms

162 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:

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

Type:

Genome binding/occupancy profiling by high throughput sequencing

11 related Platforms

154 Samples

Download data: BROADPEAK, NARROWPEAK

(Submitter supplied) The causal agent of bacterial wilt is Ralstonia solanacearum (Rs) with an unusually wide host range including potato. Bacterial wilt is the most destructive bacterial disease of plants that seriously reduce crop yield word-wide. Control of Rs through resistance breeding and biotechnology is considered to be very important and necessary. Rs resistance has been reported in a few potato cultivars and hybrids. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

16 Samples

Download data: TXT

(Submitter supplied) The general aim was to better understand the role of StTGA2.1 in plant immunity by transcriptional profiling of plants overexpressing the salicylic acid pathwas related TGA transcription factor StTGA2.1 after infection with potato virus Y (PVY). Potato non-transgenic cultivar Rywal (NT), Rywal-NahG (NahG), a transgenic line unable to accumulate SA due to salicylate hydroxylase expression, and a transgenic Rywal-NahG line inducibly overexpressing StTGA2.1 (TGA2.1-NahG) using the glucocorticoid-system, in which target gene expression can be controlled by external application of dexamethasone (DEX), were used. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

24 Samples

Download data: XLSX

(Submitter supplied) Tuber bruising in tetraploid potatoes (Solanum tuberosum) is a trait of economical importance, as it affects tubers' fitness for sale. Understanding the genetic components affecting tuber bruising is a key step in developing potato lines with increased resistance to bruising. As the tetraploid setting renders genetic analyses more complex, there is still a lot to learn about this complex phenotype. Here, we used genotype by sequencing data on a panel of half-sibling populations from a breeding programme to perform a genome-wide association analysis for tuber bruising. In addition, we collected transcriptomics data to enrich the GWAS results, by performing a differential expression analysis between samples with high- and low-bruising susceptibility.

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

100 Samples

Download data: CSV

(Submitter supplied) Small RNAs, including microRNAs (miRNAs), phased secondary small interfering RNAs (phasiRNA), and heterochromatic small interfering RNAs (hc-siRNA) are an essential component of gene regulation. To establish a broad potato small RNA atlas, we constructed an expression atlas of leaves, flowers, roots, and tubers of Desiree and Eva, which are commercially important potato (Solanum tuberosum) cultivars. more...

Organism:

Solanum tuberosum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL32683

24 Samples

Download data: TXT

(Submitter supplied) Background: A reasonable supply of nitrogen (N) fertilizer is essential for obtaining high-quality, high-level, and stable potato yields, and an improvement in the N utilization efficiency can effectively reduce N fertilizer use. It is important to use accurate, straightforward, and efficient transgenic breeding techniques for the identification of genes that can improve nitrogen use efficiency, thus enabling us to achieve the ultimate goal of breeding N-efficient potato varieties. more...

Organism:

Solanum tuberosum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22257

48 Samples

Download data: XLSX

(Submitter supplied) Leaves of the potatoes grown for 3 and 8 weeks at NT and HT were harvested for total RNA extraction. Total RNA was extracted from 100 mg of ground leaves using the Trizol reagent (MRC) following the manufacturer’s instructions. Five micro gram of each RNA sample were generated for a strand-specific library as previously described. The library was containing inserts of 150-200 bp. For RNA sequencing, paired-end 150 nt sequencing was performed using a HiSeq 4000 platform (Illumina, USA) at Microgen (Korea).

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27423

12 Samples

Download data: XLSX

(Submitter supplied) GIGANTEA (GI) is a plant-specific, circadian clock-regulated, nuclear protein with pleiotropic functions studied in many plant species. It is involved in flowering, circadian clock control, chloroplast biogenesis, carbohydrate metabolism, stress responses and synthesis of volatiles. In potato (Solanum tuberosum L.), however, only its role in tuber initiation is reported. Based on the findings in other plant species we hypothesized that the function of GI is not restricted to tuberization in potato. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27910

6 Samples

Download data: TXT

(Submitter supplied) Purpose: observe the difference between potato (Solanum tuberosum ssp. andigena) WT and BRC1b RNAi axillary buds in response to the transition from long-day to short-day conditions. The time course includes four time points: Long days, after 2 days in short days, 1 week in short days and 2 weeks in short days. Methods: stem were flash-frozen in N2(l) one hour after dawn and the axillary buds were dissected in the cold room. more...

Organism:

Solanum tuberosum subsp. andigenum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28973

24 Samples

Download data

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

Organism:

Solanum tuberosum

Type:

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

Platform:

GPL22257

24 Samples

Download data: TXT

(Submitter supplied) The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, the content of anthocyanin was measured in four potato varieties (B, R, Y and W) and genes regulating anthocyanin synthesis in different potato varieties were identified by comparing transcriptomic approaches. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22257

12 Samples

Download data: TXT

(Submitter supplied) The anthocyanin glycosides in potato tubers not only provide the plant with bright color and high nutritional value, but also have pharmacological effects such as antioxidant, hypotensive, lipid-lowering and immunity-boosting. However, the regulatory mechanism of anthocyanin in potato tubers is still unclear. In this study, twelve miRNA libraries, three of which are from the Red beauty (R-1, R-2 and R-3), three of which are from the Black kingkong (B-1, B-2 and B-3), three of which are from the Longshu No.7 (Y-1, Y-2 and Y-3) and three of which are from the LK77 (W-1, W-2 and W-3), were constructed and analyzed by high-throughput sequencing. more...

Organism:

Solanum tuberosum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL22257

12 Samples

Download data: TXT

(Submitter supplied) There is a need for expansion of the available potato genomic and transcriptomic resources in order to explore novel traits for potato improvement. Transcriptomic data derived from leaves from eleven native South American potato landraces (ten Peruvian and another; TBR Chilean) has been collected in order to aid the annotation of these genomes.

Organism:

Solanum tuberosum; Solanum x curtilobum; Solanum stenotomum subsp. stenotomum; Solanum tuberosum subsp. andigenum; Solanum phureja; Solanum stenotomum subsp. goniocalyx; Solanum x juzepczukii; Solanum chaucha; Solanum ahanhuiri

Type:

Expression profiling by high throughput sequencing

9 related Platforms

11 Samples

Download data: FPKM_TRACKING

(Submitter supplied) Glycoalkaloids are Solanum bioactive compounds and are involved in allelopathic interactions. To achieve a better understanding of plant–plant interactions, it is essential to deeply examine the trait distribution in a segregating population. In the present paper, we used transcriptomic and metabolomic approaches to recognize the phytotoxic abilities of potato plants originating from a diploid segregating F1 population with particular emphasis on glycoalkaloids in potato groups characterized by a high glycoalkaloid content. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28958

9 Samples

Download data: CSV, XLS

(Submitter supplied) For the first time, we report differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in potato (Solanum tuberosum L.) tubers characterized by light and dark chip color after cold storage. Two potato diploid progenies derived from reciprocal crosses of parental clones possessing the T- and D-type cytoplasm were used. We recognized 48 and 15 DEGs as compared to RNA-seq data of contrasting segregants. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28958

12 Samples

Download data: XLSX

(Submitter supplied) Phytophthora spp. encode large sets of effector proteins and distinct populations of small RNAs (sRNAs). Reports suggest that pathogen-derived sRNAs can modulate the expression of plant defense genes. The experiments reported here were designed to shed light on impact of sRNAs in the potato-P. infestans interaction. We used the Argonaute or Ago1 from P. infestans tagged with GFP transformed into the 88069 strain to infect potato cv. more...

Organism:

Solanum tuberosum; Phytophthora infestans

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL21069 GPL25509

12 Samples

Download data: TXT

(Submitter supplied) Transcriptome sequencing was performed to reveal the physiological changes of potato tubers after injury at the transcriptome level

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16436

8 Samples

Download data: TXT

(Submitter supplied) The periderm is a protective barrier crucial for land plants survival, but genetic factors involved in its regulation are fairly unknown. In a previous transcriptomic approach in the cork oak periderm (Quercus suber) we identified a RS2-INTERACTING KH PROTEIN (RIK) homolog, of unknown function and with a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. To gain insight into the function of RIK in periderm, the potato (Solanum tuberosum) tuber periderm was used as a model. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16436

12 Samples

Download data: CSV