Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression study after 3 days of cold exposure in a Solanum tuberosum cultivar called Desirée

ABSTRACT: The molecular response to cold exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon cold exposure in Desirée leaves were observed in the photosynthesis-related genes, which were down-regulated, whereas cell rescue, detoxication and transcription factor-related genes were mostly up-regulated. We also observed an increased expression of polyamine and proline synthesis-related genes, as well as some carbohydrate-related genes such as sucrose synthase and trehalose-6-phosphate synthase. Gene expression was followed at day 3 after the beginning of the treatment: cold (4°C) and control conditions. For each condition, 4 independent biological replicates were sampled.

ORGANISM(S): Solanum tuberosum

SUBMITTER: Danièle Evers

PROVIDER: E-GEOD-34110 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression study after 3 days of cold or salt exposure in a Solanum tuberosum cultivar called Desirée

Project description:This SuperSeries is composed of the following subset Series: GSE34110: Gene expression study after 3 days of cold exposure in a Solanum tuberosum cultivar called Desirée GSE34116: Gene expression study after 3 days of salt exposure in a Solanum tuberosum cultivar called Desirée Refer to individual Series

2011-12-03 | E-GEOD-34118 | biostudies-arrayexpress

Gene expression study after 3 days of salt exposure in a Solanum tuberosum cultivar called Desirée

Project description:The molecular response to salt exposure was studied in the leaves of an S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed, whereas cell rescue and transcription factor-related genes were mostly up-regulated. A strong down-regulation of several functional categories including primary metabolism, detoxication apparatus and signal transduction was also observed. Gene expression has been followed three days after salinity treatment (150 mM NaCl). For each condition, 4 independent biological replicates were sampled. Dye-swaps were performed.

2011-12-03 | E-GEOD-34116 | biostudies-arrayexpress

Gene expression study after 1 and 3 days of salt exposure in a Solanum tuberosum cultivar called PS3

Project description:The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level. Gene expression has been followed at two different time-points (one and three day after salinity treatment) and conditions: salt-treatment (150 mM NaCl) and control conditions. For each time-point and conditions 3 independent biological replicates were sampled.

2010-05-05 | E-GEOD-18053 | biostudies-arrayexpress

Transcriptomes profile of Solanum tuberosum (St) and Solanum commersonii (Sc) under cold stress and AtCBF3 overexpression.

Project description:St (common potato) is a freezing sensitive species unable to cold acclimate. The close wild relative Sc is freezing tolerant and able to cold acclimate. Here we compare the cold transcriptome of these two species with different levels of freezing tolerance. We also identify the putative CBF regulons by comparing the transcriptomes of wild type plants with that of 35S::AtCBF3 transgenic lines in both species. Plants were grown in 16:8 photoperiod. Eight hours after dawn, plants were either transfered to cold or kept in the warn. Wild type S. tuberosum and S. commersonii were grown at 2oC for 2h, 24h and 7 days. Wild type plants grown under warm temperatures for 2h was used as control for 2h cold samples; wild type warm grown plants for 24h were used as controls for 24h and 7 days cold samples. Under warm conditions, S. commersonii 35S::AtCBF3 lines were compared to S. commersonii wild type plants (same thing was done for S. tuberosum).

2011-04-30 | E-GEOD-22449 | biostudies-arrayexpress

Comparative genomic hybridization of 17 Borrelia burgdorferi isolates of varying pathogenicity and RST gene type to investigate genome plasticity

Project description:B. burgdorferi isolates differ in pathogenicity, and a correlation between RST type and pathogenicity was observed: the most invasive of the isolates are associated with RST1 and the least invasive with RST3 (Wang et al. 2001, Wang et al. 2002, Wormser et al. 1999). Comparative genome hybridization employing custom B. burgdorferi 70mer oligonucleotide microarrays representing all reference strain B31MI ORFs was used to assess genome plasticity, to reveal genes that are conserved and thus may encode essential functions and to reveal elements encoding potential virulence factors in 15 B. burgdorferi isolates (B479, B515, BL206, 297, B376, B379, BL224, B331, B348, B356, B408, B418, B500, JD1, N40) representing all three RST types. Total genomic DNA for each isolate was labeled with cy3 and hybridized simultaneously with cy5-labeled B31MI DNA as reference. Each hybridization was performed in duplicate.<br> Microarray quality was determined by preliminary hybridizations with reference B31MI DNA labeled with both cy3 and cy5. The specificity of the arrays was assessed by cohybridization of cy-3 labeled DNA from strain B314, a B31 derivative lacking linear plasmids (Sadziene et al. 1993), with cy5-labeled B31MI DNA.

2006-08-15 | E-MEXP-735 | biostudies-arrayexpress

Microarray based molecular marker detection

Project description:Fungal resistant and susceptible maize genotypes were subjected to Aspergillus flavus spore inoculation and kernels around the infected area were collected 4 days after inoculation. Uninoculated kernels were also collected at 4 days. Microarray experiment was performed to compare the transcriptional profiles of the different genotypes and interpret the genes involved in the associated resistance of the individual genotype to further characterize them as potential molecular markers for resistance.

2011-09-15 | E-MTAB-766 | biostudies-arrayexpress

Operon Stromal upregulation of lateral epithelial adhesions

Project description:Microarray analysis was used to identify genes that were differentially expressed when epithelial cells were grown in 3D Matrigel culture with stromal co-culture compared to without stroma.

2011-01-01 | E-MEXP-2994 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts using antibodies raised against OE17 and OE23 chloroplast targeted proteins

Project description:OE17 and OE23 are chloroplast targeted proteins. RNA co-immunoprecipitation was performed using antibodies raised against these proteins. RNA from the pellet and from the supernatent for each pulldown was labeled with different fluoro-dyes.

2006-09-01 | E-MEXP-784 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts prepared from wild type and PPR4-deficient tissue

Project description:Co-immunoprecipitation of the maize pentatricopeptide protein PPR4 and extraction of bound RNA. RNA is labelled and hybridized to a maize chloroplast genome tiling array in order to identify target RNA species of PPR4.

2022-11-22 | E-MEXP-716 | biostudies-arrayexpress

Chromatin immunoprecipitation of RNA binding protein CFM2 in Zea mays chloroplast extracts

Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CFM2 in Zea mays. CFM2 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue are likely targets for CFM2.

2006-09-01 | E-MEXP-743 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data