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GSE16457
Triticum aestivum
10 Downloadable Samples
Affymetrix Wheat Genome Array (wheat)
Description
affy_seed_kinetic_wheat - affy_seed_kinetic_wheat - Study gene expression during the grain developmental -The aim of the study is to identify the genes that are differentially expressed during the grain development in wheat.-Study gene expression during the grain developmental Sample at 100 degree days, year 2004 and 2006 Sample at 200 degree days, year 2004 and 2006 Sample at 250 degree days, year 2004 and 2006 Sample at 300 degree days, year 2004 and 2006 Sample at 400 degree days, year 2004 and 2006
Publication Title
RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 8 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
Two-week old rice plants (cultivar Nipponbare) were treated with either Magnaporthe grisea (virulent isolate FR13) spore suspension in gelatine or gelatine alone. Two time points were taken (3 and 4 days post inoculation- dpi). Disease symptoms were not visible at 3 dpi whereas they were at 4 dpi. Two biological repeats were done.
Publication Title
Susceptibility of rice to the blast fungus, Magnaporthe grisea.
Sample Metadata Fields
No sample metadata fields
View Samples- Gallus gallus
- 8 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development. The study was performed using two complementary approaches: a descriptive study of standard laying hens and then a differential study performed with hens from experimental lines expressing broad variations of achieved fertility (approximately 20 per cent). A differential kinetic study is performed on INRA lines selected on the basis of their fertility potential in purpose of hopefully access gene markers of fertility performance.
Publication Title
Identification of germinal disk region derived genes potentially involved in hen fertility.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 9 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
affy_xoo_rice - affy_xoo_rice - The Bacterial Leaf Blight disease of rice is due to Xanthomonas oryzae pv. oryzae. As for many pathogenic bacteria, it relies on a type 3 secretion system that is devoted to the injection of type 3 effectors into the eukaryotic host cell. These proteins are meant to suppress host basal defense responses and/or mimic some host regulatory function promoting bacterial survey in the plant. We are interested in the functional analysis of a subgroup of Xoo T3Es, that are specialized in host cell transcriptome remodelling. These effectors, therefore called TAL for Transcription Activator-Like proteins (also named AvrBs3/PthA-like), are often key virulence factors essential to Xoo pathogenicity such as the effector protein Talc of african Xoo strain BAI3. Our goal is to understand its function during disease development, by identifying rice host genes that are being directly up- or down-regulated by Talc. To that end, we aim at performing Affymetrix transcriptomic analysis, comparing leaf samples of a susceptible rice line inoculated with Xoo to leaves challenged with a Talc-deficient mutant and water-treated leaves. Highly induced genes are likely to be Talc primary targets and therefore potentially good susceptibility gene candidates.-The goal of the experiment is to identify the rice genes up- or down-regulated by the type III effector Talc from Xoo African strain BAI3, upon the inoculation of susceptible rice leaves 24 hours post-infection. To that end, the experimental design includes the inoculation of Nipponbare rice leaves with the virulent Xoo strain BAI3, that will be compared to Nipponbare rice leaves inoculated with a talc K.O. mutant strain and water.
Publication Title
Colonization of rice leaf blades by an African strain of Xanthomonas oryzae pv. oryzae depends on a new TAL effector that induces the rice nodulin-3 Os11N3 gene.
Sample Metadata Fields
Specimen part
View Samples- Gallus gallus
- 6 Downloadable Samples
- Affymetrix Chicken Genome Array (chicken)
Description
The aim of this study was to assess the impact of oocyte competence on subsequent fertility. Based on knowledge already accessible in mammals and on bioinformatics tools including the chicken genome sequence, we focused on the expression of genes involved in the processes of fertilization and of early embryo development.
Publication Title
Search for the genes involved in oocyte maturation and early embryo development in the hen.
Sample Metadata Fields
No sample metadata fields
View Samples- Oryza sativa
- 35 Downloadable Samples
- Affymetrix Rice Genome Array (rice)
Description
affy_rice_2011_03 - affy_compartimentation_rice_albumen_embryon - During germination, the rice seed goes from a dry quiescent state to an active metabolism. As with all cereals, the rice seed is highly differentiated between the embryo (that will give rise to the future plantlet) and the endosperm (that contains the seed storage compounds and that will degenerate). The molecular mechanisms operating in the rice seed embryo have begun to be described. Yet, very few studies have focused specifically on the endosperm during the germination process. In particular, the endosperm is mostly addressed with regards to its storage proteins but we have detected a large protein diversity by two-dimensional electrophoresis. Similarly, the endosperm is rich in total RNA which suggest that gene expression coming from seed maturation could play a role during the germination process. In this context, we want to compare the transcriptome of the embryo and the endosperm during rice seed germination. -We germinate rice seeds of the first sequenced rice cultivar i.e. Nipponbare during 0, 4, 8, 12, 16 and 24h of imbibition in sterile distilled water. Germination occurs under constant air bubbling, in the dark at 30C. These rice seeds are then manually dissected into embryo and endosperm fractions. -The embryo-derived samples are abbreviated in E while the endosperm samples are abbreviated A. The germination time-point is indicated after the letter (e.g. E8 for embryo samples harvested after 8 hours of germination). Finally, the biological repetition number is indicated before the letter and the time digit (e.g. 1-E8 for an embryo sample from the first repetition at 8 hours of imbibition).
Publication Title
Compartmentation and dynamics of flavone metabolism in dry and germinated rice seeds.
Sample Metadata Fields
Specimen part
View Samples- Zea mays
- 4 Downloadable Samples
- Affymetrix Maize Genome Array (maize)
Description
At 35 DAP whole kernels (pericarp + endosperm + embryo) without glumes of green house grown ears of heterozygous (+/bt2-H2328), self-pollinated plants were visually divided into pools of phenotypically normal looking kernels (small indentation, slightly smaller than mutant kernels, genotype +/+ or +/bt2-H2328) and pools of phenotypically mutant kernels (plump, round kernels, slightly larger than normal kernels, genotype bt2-H2328/bt2-H2328). Pools consisted of 4 kernels. 3 different ears were used for a biological duplicate.
Publication Title
Transcriptional and metabolic adjustments in ADP-glucose pyrophosphorylase-deficient bt2 maize kernels.
Sample Metadata Fields
No sample metadata fields
View Samples- Populus x canadensis
- 16 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
affy_popsec_nancy_roots_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-Two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. Four to eight root apices (1cm-long) were collected on each individual tree. Total RNAs were extracted from all roots for each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment.
Publication Title
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.
Sample Metadata Fields
Specimen part
View Samples- Populus x canadensis
- 16 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2007_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affimetrix slide.
Publication Title
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.
Sample Metadata Fields
Specimen part
View Samples- Populus x canadensis
- 8 Downloadable Samples
- Affymetrix Poplar Genome Array (poplar)
Description
affy_popsec_nancy_leaves_poplar - affy_popsec_nancy_leaves2008_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in mature leaves, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. During water deficit, leaves underwent many processes aiming to maintain cells integrity such as water status adjustment through osmoregulation or cell detoxication. These analyses intend to identify genes of interest involved in homeostasis maintenance. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to discriminate genes presenting a potential adaptative character from genes responding passively to the constraint-In a first experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. In a second experiment, two poplar clones, Soligo (S) and Carpacio (C) were submitted to 2 treatments: control and moderate water deficit. Mature leaves were collected and total RNAs were extracted from each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide.
Publication Title
Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes.
Sample Metadata Fields
Specimen part
View Samples