Ontology highlight
ABSTRACT:
PROVIDER: PRJNA340243 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate changes in genome methylation in flax seedlings under drought stress, we selected a drought-tolerant flax variety (Z141) and a drought-sensitive flax variety (NY-17) We then performed genome methylation analysis using data obtained from Z141 and NY-17 leaf tissue BS-seq at four different treatments (DS, RW, RD and CK).
2023-07-14 | GSE213719 | GEO
Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages.
2010-06-15 | GSE21868 | GEO
Project description:To investigate theinfluence of Flax rust effectors on gene expression when transiently overexpressed in flax leaves.
2022-07-13 | GSE207874 | GEO
Project description:We developped a new oligo microarray platform to analyse flax transcriptome. Here, we validated this microarray on several tissues of flax, at different developmental stages. 30 chips study using total RNA from 9 different tissue samples of Flax (Leaf sample at green capsule stage, stem inner tissue at vegetavie stage, stem outter tissue at vegetative stage, stem inner tissue at green capsule stage, stem outter tissue at green capsule stage, roots, embryos of 10, 20 and 40 days after flowering) for an overall survey of microarry accuracy and total RNA from 6 stem tissue at green capsule stage (3 of the cultivar 'Belinka' and 3 of the cultivar 'Drakkar') for an analysis of biological replicates reproducibility.
2010-06-15 | E-GEOD-21868 | biostudies-arrayexpress
Project description:Imbalanced nutrition and exogenous gonadotrophins affect uterine function and morphology. In sheep, FSH-induced superovulation causes morphological alterations in the uterus, leading, i.e., to an increase in lipid droplets. Similarly, depending on diet, FSH treatment alters the expression of estrogen and progesterone receptors and of adhesion molecules. To broad the knowledge regarding imbalanced nutrition and carry-over effects of superovulation induced with FSH in the caruncular endometrium, deep RNA sequencing (NGS, RNA-Seq) was applied, followed by functional analysis. Ewes (n = 3-5/group) were divided as follows: control fed (CF), overfed (OF), and underfed (UF), and each group was further treated with FSH (superovulated (SOV)) or saline (negative controls (CONT)). Samples were collected on day 10 of diestrus. Furthermore, samples from CF_CONT were collected on day 5 to assess time-dependent changes. The 1484 differentially expressed genes (DEGs, P < 0.01, FDR < 0.05) identified between CF_CONT animals at days 5 and 10 were associated with increased immune activity and cellular metabolic processes and decreased cellular proliferation. In CONT animals, unbalanced nutrition (i.e., both OF and UF) was associated with enrichment of terms associated with cell adhesion and differentiation, immune response and angiogenesis. As for carry-over effects of FSH, higher number of DEGs were found for CF animals (1374), than in OF (168) or UF (18) samples, associated with dysregulation of cell cycle and hormonal sensitivity. The absence of genes concomitantly affected by SOV at all different feeding regimes suggested multidirectional and body condition-dependent effects of FSH in caruncular transcriptome. Both body condition and SOV appear to affect the homeostasis of the ovine caruncles, possibly involving the modulation of uterine receptivity.
2024-04-19 | GSE229048 | GEO
Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology We compared two categories of flax target probes: short (25-mers) oligonucleotides and long (60-mers) oligonucleotides in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. This comparison was realized with two different flax samples and each RNA sample was used for the two categories of arrays. Experiments were realized in order to discriminate specific gene expression profiles of two different flax tissues (outer and inner stem tissues).
2012-05-14 | E-GEOD-37980 | biostudies-arrayexpress
Project description:Proteomic analyses of four different flax organs/tissues (inner-stem, outer-stem, leaves and roots) enriched in proteins from 3 different sub-compartments (soluble-, membrane-, and cell wall-proteins) was combined with publically available data on flax seed and whole-stem proteins to generate a flax protein database containing 2996 non-redundant total proteins. Examination of the proteins present in different flax organs/tissues provided a detailed overview of cell wall metabolism and highlighted the importance of hemicellulose and pectin remodeling in stem tissues.
2017-07-19 | PXD005003 | Pride
Project description:Whole-genome bisulfite sequencing (WGBS) was employed for identification of differential DNA methylation profiles among control and heat-stressed seedlings of a fibre flax (Linum usitatissimum L.) var., JRF-2. It was identified as a tolerant variety of heat stress-induced oxidative damage. High-quality genomic DNA from four samples comprised 3-week-old control and heat-stressed (40±2°C) seedlings, with or without treated with 5-Azacytidine (hypomethylating agent). High-quality and filtered paired-end Illumina reads were aligned to the flax reference genome, assembled in chromosomes, using bwa-meth tool, followed by methylation loci (5-mC) calling using the MethylDackel software. Differentially methylated regions (DMRs) between the control and other samples were identified using the methylKit and annotated using genomation package for their precedence in the promoter/exon/intron/intergenic regions. The DMRs comprised both hyper- and hypomethylated loci, but the latter found dominated due to heat stress in flax seedlings. The WGBS in flax for heat stress will provide a platform to identify epigenetic loci responsible for heat-stress adaptation in flax.
2022-04-01 | GSE185571 | GEO
Project description:Performances of flax gene expression analyses were compared in two categories of Nimblegen microarrays (short 25-mers oligonucleotides and long 60-mers oligonucleotides) Results obtained in this study are described in Intra-platform comparison of flax (Linum usitatissimum L.) high-density Nimblegen DNA microarrays submitted to Journal of Computational Biology
2012-05-15 | GSE37980 | GEO
Project description:In the present study, the miRNA expression changes in the maritime pine roots from seedlings of one-month old under different levels of ammonium nutrition was analyzed.
2022-01-31 | GSE195700 | GEO