Geocaulosphere soil of potato tubers
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA983567 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24914500_1.fastq.gz | Fastqsanger.gz | |||
| SRR24914500_2.fastq.gz | Fastqsanger.gz | |||
| SRR24914501_1.fastq.gz | Fastqsanger.gz | |||
| SRR24914501_2.fastq.gz | Fastqsanger.gz | |||
| SRR24914502_1.fastq.gz | Fastqsanger.gz |
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Project description:Potato geocaulosphere soil Raw sequence reads
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Project description:Transcriptome sequencing was performed to reveal the physiological changes of potato tubers after injury at the transcriptome level
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Project description:This is a study to characterize gene expression profiles in stored Russet Burbank potato tubers. Tubers were harvested from commercial fields in the central sands region of Wisconsin in the fall of 2006. The tubers were put into storage at 55 degrees F for preconditioning and wound healing. Shortly after the temperature of the storage bin began to decrease, uniform, healthy tubers were selected for use in this microarray analysis. Tubers were at 53.6 degrees F at this time, and pieces of starch-storing tissue were collected for use as the reference sample. Other tubers were moved to temperature-controlled lockers and these were cooled gradually to either 48 or 40 degrees F following industry standard procedures. The expectation was that tubers held at 48 degrees would not have a significant accumulation of glucose and fructose, but that tubers cooled to 40 degrees would undergo low temperature sweetening and accumulate glucose and fructose to a degree that is unsuitable for processing. Three weeks later, when the locker temperatures were 48 degrees F and 41.5 degrees F, tissue samples were collected for RNA analysis. After another three weeks, samples were collected from tubers at 48 degrees F and 40 degrees F. At that time some tubers were moved from the 48 degree locker to the 40 degree locker in order to see if gene expression changes observed as a result of gradual cooling are similar to those that occur following a sudden decrease in temperature. Three weeks later, samples were collected from tubers held at 48 degrees F, tubers held at 40 degrees F, and from the tubers that were moved from 48 to 40 degrees F. At this time another set of tubers was transferred from 48 degrees to 40 degrees. Three weeks later the last samples were harvested from tubers held at 48 degrees F, from tubers held at 48 degrees F and from tubers that were transferred three weeks prior from 48 to 40 degrees. RNA was isolated from tissue extracted from three tubers. Keywords: Reference design
2008-02-13 | GSE10483 | GEO
Project description:Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.
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Project description:Commercial storage of potatoes often relies on the use of sprout inhibitors to prolong storage and reduce spoilage. The compound 1,4-dimethylnaphthalene (DMN) has seen increase application as a sprout inhibitor in the potato industry as older chemistries are being phased out. The mode of action of DMN is poorly understood as is the sensitivity of potato tissues to this new class of inhibitor. During storage potato tubers transition from a state of endo-dormant to eco-dormant and it is not known if the DMN response is consistent across this developmental transition. RNA-seq gene expression profiling was used to establish if stored potato tubers (Solanum tuberosum cv La Chipper) have differential sensitivity to DMN as tubers age. DMN was applied at three different times during storage; just after harvest when tubers are in endo-dormancy, midwinter at early eco-dormancy, and in spring during late eco-dormancy when sprouting was prevented via exposure to cold storage temperatures. Changes in gene expression were lowest during endo-dormancy while midwinter and spring treatments exhibited a greater and more diverse expression response. Functional analysis of differential gene expression demonstrated gene sets associated with DNA replication, cell division, and DNA methylation are suppressed after DMN treatment. However, gene sets associated with salicylic acid, jasmonic acid, abiotic and biotic stress responses are elevated by DMN only after endodormancy terminates. Gene clusters associated with pathogenesis related proteins PR-4 and PR-5 are also upregulated in response to DMN. These results indicate that DMN sensitivity changes as potato tubers age and transition from endo-dormant to eco-dormant in storage and the overall response is a shift in gene classes that regulate growth and response to stress.
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Project description:Potato soil microorganisms Raw sequence reads
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Project description:RNA was sequenced from commercially grown greenhouse minitubers treated with 10 ug of 1-(alpha-ethylbenzy)-3-nitroquanidine (NG) in DMSO and followed for four, and seven days post treatment. Control tubers were injected with DMSO alone. Sequence reads were mapped to the potato genome (PGSC_DM_v3_2.1.11) and transcript abundance was determined using Cuffdiff v 2.02.
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Project description: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. A total of 167.3 M of clean reads were obtained. After the raw reads were subjected to quality control and filtering, 151,010,820 clean tags were obtained from the twelve libraries. The filtered reads were subsequently compared with the updated potato reference genome, and the vast majority of effective reads were successfully mapped. The mapped reads from the twelve libraries covered 77.10-84.48% of the potato genome, therefore, the analysis based on the genome was considered reliable. The lengths of the obtained miRNAs were further analysed to find that 64% of the miRNAs were concentrated at 21bp in length, followed by a higher number of miRNAs at 22bp and 24bp in length.
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